diff --git a/Ranking/DPPC_ranking.csv b/Ranking/DPPC_ranking.csv index cd2e0e94d0..e8d41a051d 100644 --- a/Ranking/DPPC_ranking.csv +++ b/Ranking/DPPC_ranking.csv @@ -1,6 +1,11 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 728,CHARMM36-LJPME,DPPC (1),323.0,31.0,0.7403,0.7976,,0.7976 +935,prosECCo 75 paper related data,DPPC (1),324.0,45.0,0.4525,0.6585,,0.6585 +934,prosECCo 75 paper related data,DPPC (1),322.0,45.0,0.1789,0.6571,,0.6571 +931,prosECCo 75 paper related data,DPPC (1),323.0,45.0,0.4128,0.6561,,0.6561 463,Slipids,DPPC (1),323.0,30.0,0.5802,0.6369,,0.6369 +936,prosECCo 75 paper related data,DPPC (1),321.0,45.0,0.0262,0.6337,,0.6337 +933,prosECCo 75 paper related data,DPPC (1),320.0,45.0,,0.6118,,0.6118 911,CHARMM36,DPPC (1),322.0,41.1,0.2489,0.5992,,0.5992 319,CHARMM36,DPPC (1),323.0,30.4,0.3746,0.5944,,0.5944 390,GAFFlipid,DPPC (1),323.0,30.5,0.3819,0.5881,,0.5881 diff --git a/Ranking/FF_ranking.csv b/Ranking/FF_ranking.csv index ab21e46b2e..81bae17f29 100644 --- a/Ranking/FF_ranking.csv +++ b/Ranking/FF_ranking.csv @@ -22,8 +22,8 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 748,Charmm-Drude polarizable,POPC (1),303.0,31.1,0.9421,,, 545,Poger GROMOS 53A6_L; Reaction Field for computing electrostatics,DPPC (1),323.0,45.6,0.9353,0.0566,0.0,0.0566 666,Lipid17,CHOL:POPC (1:4),298.15,50.0,0.9275,,, -338,Slipids,POPS (1),298.0,35.0,0.9223,0.1626,0.1717,0.1444 443,"ECC-lipids, SPC water model, ECC-ions",POPS (1),298.0,50.0,0.9223,0.4953,0.6622,0.1614 +338,Slipids,POPS (1),298.0,35.0,0.9223,0.1626,0.1717,0.1444 400,GROMOS-CKP,POPE (1),310.0,50.0,0.9186,0.4566,0.5374,0.2949 38,Orange,POPC (1),298.0,40.0,0.9079,0.2557,0.3691,0.0287 103,ECC-lipids,POPC (1),313.0,50.0,0.9053,,, @@ -91,7 +91,9 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 47,CHARMM36,DOPC (1),303.15,50.0,0.4967,0.6186,0.607,0.6416 674,MacRog,POPC (1),298.15,50.0,0.493,0.665,0.6968,0.6013 551,CHARMM36,DOPC (1),303.15,50.0,0.4823,0.5898,0.5656,0.6381 +932,prosECCo 75 paper related data,DPPC (1),325.0,45.0,0.4703,,, 457,MacRog,POPC (1),300.0,40.0,0.4673,0.6676,0.6858,0.6312 +935,prosECCo 75 paper related data,DPPC (1),324.0,45.0,0.4525,0.6585,0.0,0.6585 316,CHARMM36,DOPC (1),303.15,50.0,0.4512,0.5558,0.5112,0.6449 87,CHARMM36,DPPC (1),325.0,40.0,0.4412,,, 63,MacRog,POPC (1),298.0,50.0,0.4335,0.5974,0.5853,0.6216 @@ -99,6 +101,7 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 702,MacRog,CHOL:POPC (1:4),298.15,50.0,0.4304,,, 533,CHARMM36,POPC (1),303.0,31.1,0.4256,,, 915,CHARMM36/LJ-PME,DLPC (1),293.0,43.1,0.4148,,, +931,prosECCo 75 paper related data,DPPC (1),323.0,45.0,0.4128,0.6561,0.0,0.6561 390,GAFFlipid,DPPC (1),323.0,30.5,0.3819,0.5881,0.0,0.5881 658,MacRog,POPC (1),298.15,50.0,0.3818,0.6963,0.707,0.6749 319,CHARMM36,DPPC (1),323.0,30.4,0.3746,0.5944,0.0,0.5944 @@ -133,6 +136,7 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 790,Charmm36,POPE (1),310.0,40.0,0.2055,0.1891,0.0974,0.3724 687,Slipids,CHOL:POPC (1:4),298.15,50.0,0.2024,,, 914,CHARMM36/LJ-PME,DLPC (1),303.0,43.1,0.1916,,, +934,prosECCo 75 paper related data,DPPC (1),322.0,45.0,0.1789,0.6571,0.0,0.6571 27,CHARMM36,DPPC (1),333.15,50.0,0.1766,0.1136,0.0,0.1136 299,Berger and Modified Höltje model for cholesterol,CHOL:POPC (1:1),298.0,80.6,0.1698,0.1702,0.1953,0.0083 305,Berger and Modified Höltje model for cholesterol,CHOL:POPC (1:15),298.0,57.0,0.1603,0.3775,0.5603,0.0118 @@ -162,6 +166,7 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 202,GROMOS-CKP,POPC (1),298.0,50.0,0.0367,0.1282,0.1742,0.0362 109,CHARMM36,CHOL:POPC (1:8),298.15,50.0,0.0337,,, 837,FF-development,POPC (1),300.0,40.0,0.0324,0.5638,0.5676,0.5561 +936,prosECCo 75 paper related data,DPPC (1),321.0,45.0,0.0262,0.6337,0.0,0.6337 673,Lipid17,CHOL:POPC (5:8),298.15,50.0,0.0189,,, 694,Lipid17,CHOL:POPC (5:8),298.15,50.0,0.0179,,, 678,CHARMM36,POPC (1),298.15,50.0,0.016,0.3912,0.2693,0.6351 @@ -181,30 +186,30 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 679,MacRog,CHOL:POPC (5:8),298.15,50.0,0.0015,,, 82,slipids,CHOL:POPC (1:1),298.0,39.7,0.0014,0.4174,0.3907,0.1765 72,CHARMM36,CHOL:POPC (1:4),298.15,50.0,0.0014,,, -832,FF-development,POPC (1),300.0,40.0,0.0007,0.2767,0.1768,0.4766 550,CHARMM36,CHOL:POPC (5:8),298.15,50.0,0.0007,,, 716,MacRog,CHOL:POPC (5:8),298.15,50.0,0.0007,,, +832,FF-development,POPC (1),300.0,40.0,0.0007,0.2767,0.1768,0.4766 525,CHARMM36,CHOL:POPC (1:4),298.15,50.0,0.0006,,, 275,CHARMM36,CHOL:POPC (5:8),298.15,50.0,0.0004,,, +620,CHARMM36,CHOL:POPC (5:8),298.15,50.0,0.0003,,, +682,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.3653,0.334,0.1681 703,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.3257,0.2892,0.1583 698,MacRog,CHOL:POPC (5:8),298.15,50.0,0.0003,,, -620,CHARMM36,CHOL:POPC (5:8),298.15,50.0,0.0003,,, 712,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.36,0.3283,0.1671 -682,Slipids,CHOL:POPC (7:8),298.15,50.0,0.0003,0.3653,0.334,0.1681 792,OpenFF,POPC (1),300.0,39.1,0.0002,0.5635,0.5485,0.5935 836,FF-development,POPC (1),300.0,40.0,0.0001,0.3347,0.4433,0.1176 704,MacRog,CHOL:POPC (7:8),298.15,50.0,0.0001,0.218,0.1541,0.175 -91,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3211,0.2694,0.1776 838,Parsley 1.3.1,POPC (1),300.0,40.0,0.0,0.183,0.0182,0.5127 -166,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3354,0.2842,0.184 -834,Sage2.2.0 Espaloma Charges,POPC (1),300.0,40.0,0.0,0.3115,0.1992,0.5361 -717,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4908,0.515,0.1699 -707,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4431,0.4592,0.1541 543,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3336,0.2788,0.1866 +707,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4431,0.4592,0.1541 +717,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4908,0.515,0.1699 +834,Sage2.2.0 Espaloma Charges,POPC (1),300.0,40.0,0.0,0.3115,0.1992,0.5361 +166,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3354,0.2842,0.184 +699,MacRog,CHOL:POPC (7:8),298.15,50.0,0.0,0.2997,0.2274,0.1863 +91,CHARMM36,CHOL:POPC (7:8),298.15,50.0,0.0,0.3211,0.2694,0.1776 835,FF-development,POPC (1),300.0,40.0,0.0,0.1023,0.0058,0.2953 +731,Charmm-Drude,POPE (1),310.0,35.0,0.0,0.2249,0.3077,0.0593 714,Lipid17,CHOL:POPC (7:8),298.15,50.0,0.0,0.4714,0.4903,0.1653 -765,Charmm36,SM16 (1),328.15,45.0,0.0,0.3412,0.3412,0.0 -699,MacRog,CHOL:POPC (7:8),298.15,50.0,0.0,0.2997,0.2274,0.1863 671,MacRog,CHOL:POPC (7:8),298.15,50.0,0.0,0.3119,0.2321,0.196 -731,Charmm-Drude,POPE (1),310.0,35.0,0.0,0.2249,0.3077,0.0593 828,Sage 2.2.1,POPC (1),300.0,40.0,0.0,0.3899,0.3101,0.5495 +765,Charmm36,SM16 (1),328.15,45.0,0.0,0.3412,0.3412,0.0 diff --git a/Ranking/OP_ranking.csv b/Ranking/OP_ranking.csv index da12e3ed07..345f3f9af9 100644 --- a/Ranking/OP_ranking.csv +++ b/Ranking/OP_ranking.csv @@ -22,6 +22,9 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 674,MacRog,POPC (1),298.15,50.0,0.493,0.665,0.6968,0.6013 800,CHARMM36,DMPC (1),314.0,5.0,,0.66,0.645,0.6901 675,MacRog,POPC (1),298.15,50.0,0.4311,0.659,0.6605,0.6558 +935,prosECCo 75 paper related data,DPPC (1),324.0,45.0,0.4525,0.6585,0.0,0.6585 +934,prosECCo 75 paper related data,DPPC (1),322.0,45.0,0.1789,0.6571,0.0,0.6571 +931,prosECCo 75 paper related data,DPPC (1),323.0,45.0,0.4128,0.6561,0.0,0.6561 715,Lipid17,POPC (1),298.15,50.0,0.8957,0.6511,0.7313,0.4905 806,CHARMM36,POPC (1),300.0,7.5,,0.6489,0.6295,0.6877 809,CHARMM36,DMPC (1),314.0,10.0,,0.6488,0.6504,0.6456 @@ -29,9 +32,11 @@ ID,FF,composition,T,Hydration,Q_FF,Q_OP,Q_OP_tails,Q_OP_heads 696,Slipids,POPC (1),298.15,50.0,0.7477,0.6426,0.669,0.5897 831,C36_Slipids_Hybrid,POPC (1),298.0,50.0,0.2142,0.6389,0.6286,0.6595 463,Slipids,DPPC (1),323.0,30.0,0.5802,0.6369,0.0,0.6369 +936,prosECCo 75 paper related data,DPPC (1),321.0,45.0,0.0262,0.6337,0.0,0.6337 810,OPLS4,DMPC (1),314.0,10.0,,0.6279,0.5503,0.7831 811,OPLS4,DMPC (1),314.0,5.0,,0.6233,0.589,0.6917 47,CHARMM36,DOPC (1),303.15,50.0,0.4967,0.6186,0.607,0.6416 +933,prosECCo 75 paper related data,DPPC (1),320.0,45.0,,0.6118,0.0,0.6118 708,Slipids,POPC (1),298.15,50.0,0.581,0.5997,0.6177,0.5637 911,CHARMM36,DPPC (1),322.0,41.1,0.2489,0.5992,0.0,0.5992 63,MacRog,POPC (1),298.0,50.0,0.4335,0.5974,0.5853,0.6216 diff --git a/Simulations/004/eb6/004eb6c414eca4dd73398e7b7218d8961c950b70/21fe6e771571ea659f629e3d2943006de7ff0dde/README.yaml b/Simulations/004/eb6/004eb6c414eca4dd73398e7b7218d8961c950b70/21fe6e771571ea659f629e3d2943006de7ff0dde/README.yaml index 9848c262a6..80f5769d0a 100644 --- a/Simulations/004/eb6/004eb6c414eca4dd73398e7b7218d8961c950b70/21fe6e771571ea659f629e3d2943006de7ff0dde/README.yaml +++ b/Simulations/004/eb6/004eb6c414eca4dd73398e7b7218d8961c950b70/21fe6e771571ea659f629e3d2943006de7ff0dde/README.yaml @@ -25,8 +25,9 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 128POPE_3552SOL_303K_v1 SOFTWARE_VERSION: 4.0.7 FF: Berger-POPE-2004 -FF_SOURCE: starting structure from equilibrated POPE membrane simulated with the GROMOS-CKP - force field, PE parameters https://pubs.acs.org/doi/abs/10.1021/jp0366926 +FF_SOURCE: >- + starting structure from equilibrated POPE membrane simulated with the GROMOS-CKP force field, PE + parameters https://pubs.acs.org/doi/abs/10.1021/jp0366926 FF_DATE: null CPT: null LOG: null diff --git a/Simulations/02e/922/02e9220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml b/Simulations/02e/922/02e9220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml index 79d100b870..56059e6d6e 100644 --- a/Simulations/02e/922/02e9220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml +++ b/Simulations/02e/922/02e9220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml @@ -8,8 +8,7 @@ EXPERIMENT: ORDERPARAMETER: POPC: [] FORMFACTOR: [] -FF_SOURCE: http://www.charmm-gui.org for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: http://www.charmm-gui.org for lipids and https://bitbucket.org/hseara/ions/ for ions COMPOSITION: SOL: NAME: TIP3 diff --git a/Simulations/046/3dd/0463dd63f8e46dc2d72690c030c3278e06899b7f/7e4185d7f1994a96d90c25772b0179b27801ea6e/README.yaml b/Simulations/046/3dd/0463dd63f8e46dc2d72690c030c3278e06899b7f/7e4185d7f1994a96d90c25772b0179b27801ea6e/README.yaml index 25ef759c11..b01a9f88e9 100644 --- a/Simulations/046/3dd/0463dd63f8e46dc2d72690c030c3278e06899b7f/7e4185d7f1994a96d90c25772b0179b27801ea6e/README.yaml +++ b/Simulations/046/3dd/0463dd63f8e46dc2d72690c030c3278e06899b7f/7e4185d7f1994a96d90c25772b0179b27801ea6e/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/07d/cf3/07dcf38cf72985a9535571aaa39d7ae76921838b/9633603ac288bf90cb41aeac480bd1b222658439/README.yaml b/Simulations/07d/cf3/07dcf38cf72985a9535571aaa39d7ae76921838b/9633603ac288bf90cb41aeac480bd1b222658439/README.yaml index 35ada5709b..08f7b81009 100644 --- a/Simulations/07d/cf3/07dcf38cf72985a9535571aaa39d7ae76921838b/9633603ac288bf90cb41aeac480bd1b222658439/README.yaml +++ b/Simulations/07d/cf3/07dcf38cf72985a9535571aaa39d7ae76921838b/9633603ac288bf90cb41aeac480bd1b222658439/README.yaml @@ -25,8 +25,9 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 336POPE_15254SOL_310K_v2 SOFTWARE_VERSION: 5.0.6 FF: CHARMM36-UA -FF_SOURCE: starting structure was made by reverse mapping an equilibrated MARTINI - POPE bilayer (constructed with the INSANE script) +FF_SOURCE: >- + starting structure was made by reverse mapping an equilibrated MARTINI POPE bilayer (constructed + with the INSANE script) FF_DATE: null CPT: null LOG: null diff --git a/Simulations/0a4/101/0a41017641414540973e921ed22528d1f3dc414b/3c0936e61fa40cce74fd1828a2697742709e91fb/README.yaml b/Simulations/0a4/101/0a41017641414540973e921ed22528d1f3dc414b/3c0936e61fa40cce74fd1828a2697742709e91fb/README.yaml index a3e2e4e775..da0c10b147 100644 --- a/Simulations/0a4/101/0a41017641414540973e921ed22528d1f3dc414b/3c0936e61fa40cce74fd1828a2697742709e91fb/README.yaml +++ b/Simulations/0a4/101/0a41017641414540973e921ed22528d1f3dc414b/3c0936e61fa40cce74fd1828a2697742709e91fb/README.yaml @@ -1,5 +1,5 @@ -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; - Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; Thalmann, Fabrice FF_DATE: June 2015 SYSTEM: 212DPPC_29826SOL_298K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/0bc/296/0bc296850dd41d32a6e9aa4ac2b5dd4e84a6605f/e64b1a6ceccc9a361529be902c17c2b4b0394484/README.yaml b/Simulations/0bc/296/0bc296850dd41d32a6e9aa4ac2b5dd4e84a6605f/e64b1a6ceccc9a361529be902c17c2b4b0394484/README.yaml index 0071ee87af..d117780a97 100644 --- a/Simulations/0bc/296/0bc296850dd41d32a6e9aa4ac2b5dd4e84a6605f/e64b1a6ceccc9a361529be902c17c2b4b0394484/README.yaml +++ b/Simulations/0bc/296/0bc296850dd41d32a6e9aa4ac2b5dd4e84a6605f/e64b1a6ceccc9a361529be902c17c2b4b0394484/README.yaml @@ -1,5 +1,5 @@ -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; - Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; Thalmann, Fabrice FF_DATE: June 2015 SYSTEM: 212DPPC_29826SOL_288K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/116/9a0/1169a0f959c9caac1671425c8ae4cd6e255dc49f/e0dbaa355f6b5faeeef73dd79514eb8364492a88/README.yaml b/Simulations/116/9a0/1169a0f959c9caac1671425c8ae4cd6e255dc49f/e0dbaa355f6b5faeeef73dd79514eb8364492a88/README.yaml index e79b4729e9..03ee381e2e 100644 --- a/Simulations/116/9a0/1169a0f959c9caac1671425c8ae4cd6e255dc49f/e0dbaa355f6b5faeeef73dd79514eb8364492a88/README.yaml +++ b/Simulations/116/9a0/1169a0f959c9caac1671425c8ae4cd6e255dc49f/e0dbaa355f6b5faeeef73dd79514eb8364492a88/README.yaml @@ -27,8 +27,7 @@ CPT: TRJLENGTH: 500100.0 TRAJECTORY_SIZE: 332189196 SOFTWARE_VERSION: 5.0.4 -FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet - and water+ions) +FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) TOP: - - DPPC_72_325K_rmcomm_leaflets_md.top PREEQTIME: 0 diff --git a/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/FormFactorQuality.json b/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/FormFactorQuality.json new file mode 100644 index 0000000000..93e1da303c --- /dev/null +++ b/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/FormFactorQuality.json @@ -0,0 +1 @@ +[0.4703, 93.0936] \ No newline at end of file diff --git a/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/README.yaml b/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/README.yaml index 79e0e46dce..84b279a961 100644 --- a/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/README.yaml +++ b/Simulations/144/922/144922f3b678f74edd34e33d582d8e90079353c6/daa44903d8c7513f82d4be1999a50f1157ae679d/README.yaml @@ -143,3 +143,8 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-23' +EXPERIMENT: + ORDERPARAMETER: + DPPC: [] + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/149/281/149281ea65b1adb21d954490f41cca37ec81c03a/c03d345271e28fc1afa559373c301ec243543886/README.yaml b/Simulations/149/281/149281ea65b1adb21d954490f41cca37ec81c03a/c03d345271e28fc1afa559373c301ec243543886/README.yaml index 86d5e5221c..dc7144d494 100644 --- a/Simulations/149/281/149281ea65b1adb21d954490f41cca37ec81c03a/c03d345271e28fc1afa559373c301ec243543886/README.yaml +++ b/Simulations/149/281/149281ea65b1adb21d954490f41cca37ec81c03a/c03d345271e28fc1afa559373c301ec243543886/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_21SOD_21CLA_370K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/164/f70/164f7048924b637b0c5113ec33c40dd9a35a6751/5c107419457aea836f8a9f6565f791e9801b2660/README.yaml b/Simulations/164/f70/164f7048924b637b0c5113ec33c40dd9a35a6751/5c107419457aea836f8a9f6565f791e9801b2660/README.yaml index 452d15da44..d94d9fb3b0 100644 --- a/Simulations/164/f70/164f7048924b637b0c5113ec33c40dd9a35a6751/5c107419457aea836f8a9f6565f791e9801b2660/README.yaml +++ b/Simulations/164/f70/164f7048924b637b0c5113ec33c40dd9a35a6751/5c107419457aea836f8a9f6565f791e9801b2660/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 86CHOL_200POPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/174/c74/174c746e212577c63e6df6c6910b2e9a1d587241/6fb923ea75663dbeea13c0fa79015ae11dea9157/README.yaml b/Simulations/174/c74/174c746e212577c63e6df6c6910b2e9a1d587241/6fb923ea75663dbeea13c0fa79015ae11dea9157/README.yaml index 5c33f0bd88..7e340c2a33 100644 --- a/Simulations/174/c74/174c746e212577c63e6df6c6910b2e9a1d587241/6fb923ea75663dbeea13c0fa79015ae11dea9157/README.yaml +++ b/Simulations/174/c74/174c746e212577c63e6df6c6910b2e9a1d587241/6fb923ea75663dbeea13c0fa79015ae11dea9157/README.yaml @@ -1,5 +1,4 @@ -AUTHORS_CONTACT: Martinez-Seara, Hector; Javanainen, Matti; Rissanen, Sami; Lolicato, - Fabio +AUTHORS_CONTACT: Martinez-Seara, Hector; Javanainen, Matti; Rissanen, Sami; Lolicato, Fabio FF_DATE: null SYSTEM: 512DPPC_20480SOL_325K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/1a3/09f/1a309f2e399c5a6ab26cad208a8b8d273a985318/3f267aa1bc067d00566db164a4edc359b33c1246/README.yaml b/Simulations/1a3/09f/1a309f2e399c5a6ab26cad208a8b8d273a985318/3f267aa1bc067d00566db164a4edc359b33c1246/README.yaml index 508d6eb926..cb86b461b5 100644 --- a/Simulations/1a3/09f/1a309f2e399c5a6ab26cad208a8b8d273a985318/3f267aa1bc067d00566db164a4edc359b33c1246/README.yaml +++ b/Simulations/1a3/09f/1a309f2e399c5a6ab26cad208a8b8d273a985318/3f267aa1bc067d00566db164a4edc359b33c1246/README.yaml @@ -9,8 +9,9 @@ PREEQTIME: 0 TIMELEFTOUT: 1000 TEMPERATURE: 310.0 SYSTEM: POPC:Gb3_run3(95:5 mol:mol) -AUTHORS_CONTACT: Alexander Vogel (alexander.vogel@medizin.uni-leipzig.de), Daniel - B. Werz (daniel.werz@chemie.uni-freiburg.de) +AUTHORS_CONTACT: >- + Alexander Vogel (alexander.vogel@medizin.uni-leipzig.de), Daniel B. Werz + (daniel.werz@chemie.uni-freiburg.de) SOFTWARE_VERSION: 2019.4/2020 FF: CHARMM36m FF_SOURCE: CHARMM-GUI diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_FragmentQuality.json b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..64e3ab489b --- /dev/null +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6561, "total": 0.6561} \ No newline at end of file diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_OrderParameters_quality.json b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..b2c28a9b73 --- /dev/null +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": NaN, + "M_G1C13_M M_G1C13H2_M": NaN, + "M_G1C14_M M_G1C14H1_M": NaN, + "M_G1C14_M M_G1C14H2_M": NaN, + "M_G1C15_M M_G1C15H1_M": NaN, + "M_G1C15_M M_G1C15H2_M": NaN, + "M_G1C16_M M_G1C16H1_M": NaN, + "M_G1C16_M M_G1C16H2_M": NaN, + "M_G1C17_M M_G1C17H1_M": NaN, + "M_G1C17_M M_G1C17H2_M": NaN, + "M_G1C17_M M_G1C17H3_M": NaN, + "M_G1C3_M M_G1C3H1_M": NaN, + "M_G1C3_M M_G1C3H2_M": NaN, + "M_G1C4_M M_G1C4H1_M": NaN, + "M_G1C4_M M_G1C4H2_M": NaN, + "M_G1C5_M M_G1C5H1_M": NaN, + "M_G1C5_M M_G1C5H2_M": NaN, + "M_G1C6_M M_G1C6H1_M": NaN, + "M_G1C6_M M_G1C6H2_M": NaN, + "M_G1C7_M M_G1C7H1_M": NaN, + "M_G1C7_M M_G1C7H2_M": NaN, + "M_G1C8_M M_G1C8H1_M": NaN, + "M_G1C8_M M_G1C8H2_M": NaN, + "M_G1C9_M M_G1C9H1_M": NaN, + "M_G1C9_M M_G1C9H2_M": NaN, + "M_G1_M M_G1H1_M": NaN, + "M_G1_M M_G1H2_M": NaN, + "M_G2C10_M M_G2C10H1_M": NaN, + "M_G2C10_M M_G2C10H2_M": NaN, + "M_G2C11_M M_G2C11H1_M": NaN, + "M_G2C11_M M_G2C11H2_M": NaN, + "M_G2C12_M M_G2C12H1_M": NaN, + "M_G2C12_M M_G2C12H2_M": NaN, + "M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.0225, + "M_G3C4_M M_G3C4H2_M": 0.0281, + "M_G3C5_M M_G3C5H1_M": 0.9463, + "M_G3C5_M M_G3C5H2_M": 0.9241, + "M_G3N6C1_M M_G3N6C1H1_M": 0.9897, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9879, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9885, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9883, + "M_G3N6C2_M M_G3N6C2H2_M": 0.988, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9889, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9884, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9889, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9877, + "M_G3_M M_G3H1_M": 0.0242, + "M_G3_M M_G3H2_M": 0.9678 + } +} \ No newline at end of file diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/FormFactorQuality.json b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/FormFactorQuality.json new file mode 100644 index 0000000000..988a264fe1 --- /dev/null +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/FormFactorQuality.json @@ -0,0 +1 @@ +[0.4128, 91.8733] \ No newline at end of file diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/README.yaml b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/README.yaml index eddd19d243..83af124e76 100644 --- a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/README.yaml +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/README.yaml @@ -143,3 +143,9 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-23' +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/SYSTEM_quality.json b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/SYSTEM_quality.json new file mode 100644 index 0000000000..b28ff5bae8 --- /dev/null +++ b/Simulations/1af/494/1af49498ed5c1f3f8f38daeb37dcd2243c79391e/bb80b1bf80b95dc4fdf84bc17c78e8f7a0000b81/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6561, "tails": 0.0, "total": 0.6561} \ No newline at end of file diff --git a/Simulations/1d9/d4f/1d9d4f9f33055b16b3b8a438fac7013ae39cc712/02048411dc25c6cb5a072f50ac939ad53b399d1c/README.yaml b/Simulations/1d9/d4f/1d9d4f9f33055b16b3b8a438fac7013ae39cc712/02048411dc25c6cb5a072f50ac939ad53b399d1c/README.yaml index 995efb676c..1a7d17003a 100644 --- a/Simulations/1d9/d4f/1d9d4f9f33055b16b3b8a438fac7013ae39cc712/02048411dc25c6cb5a072f50ac939ad53b399d1c/README.yaml +++ b/Simulations/1d9/d4f/1d9d4f9f33055b16b3b8a438fac7013ae39cc712/02048411dc25c6cb5a072f50ac939ad53b399d1c/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 22CHOL_200POPC_9000SOL_73CAL_146CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/1da/b39/1dab39c51347e2ff353297753f1e8dd86b90b6ef/119b6f2a9b4cd70c4ec19cd2e6d80eaf60dd79ad/README.yaml b/Simulations/1da/b39/1dab39c51347e2ff353297753f1e8dd86b90b6ef/119b6f2a9b4cd70c4ec19cd2e6d80eaf60dd79ad/README.yaml index 1830b0ef48..83cacfafcd 100644 --- a/Simulations/1da/b39/1dab39c51347e2ff353297753f1e8dd86b90b6ef/119b6f2a9b4cd70c4ec19cd2e6d80eaf60dd79ad/README.yaml +++ b/Simulations/1da/b39/1dab39c51347e2ff353297753f1e8dd86b90b6ef/119b6f2a9b4cd70c4ec19cd2e6d80eaf60dd79ad/README.yaml @@ -12,8 +12,7 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200DOPC_9000SOL_73CAL_146CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Kohagen for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/232/24d/23224d95390ff0e95967ea1a3d89efb1c6598d6b/4791cafeea88eda925420c35461af89656c4d659/README.yaml b/Simulations/232/24d/23224d95390ff0e95967ea1a3d89efb1c6598d6b/4791cafeea88eda925420c35461af89656c4d659/README.yaml index 79eb5e4684..17cdb45279 100644 --- a/Simulations/232/24d/23224d95390ff0e95967ea1a3d89efb1c6598d6b/4791cafeea88eda925420c35461af89656c4d659/README.yaml +++ b/Simulations/232/24d/23224d95390ff0e95967ea1a3d89efb1c6598d6b/4791cafeea88eda925420c35461af89656c4d659/README.yaml @@ -25,8 +25,9 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 128DOPE_4789SOL_271K_v2 SOFTWARE_VERSION: 4.0.7 FF: Berger-DOPE-2018 -FF_SOURCE: starting structure was converted from equilibrated DOPC membrane simulated - with GROMOS-CKP force field, https://pubs.acs.org/doi/abs/10.1021/jp0366926 +FF_SOURCE: >- + starting structure was converted from equilibrated DOPC membrane simulated with GROMOS-CKP force + field, https://pubs.acs.org/doi/abs/10.1021/jp0366926 FF_DATE: null CPT: null LOG: null diff --git a/Simulations/2a9/7d1/2a97d1e94052e72834612f60a547347514d3dfbf/c94855d55d49e55b22857b00de9012c190fe5f2e/README.yaml b/Simulations/2a9/7d1/2a97d1e94052e72834612f60a547347514d3dfbf/c94855d55d49e55b22857b00de9012c190fe5f2e/README.yaml index be4dada0ef..b10aa0705d 100644 --- a/Simulations/2a9/7d1/2a97d1e94052e72834612f60a547347514d3dfbf/c94855d55d49e55b22857b00de9012c190fe5f2e/README.yaml +++ b/Simulations/2a9/7d1/2a97d1e94052e72834612f60a547347514d3dfbf/c94855d55d49e55b22857b00de9012c190fe5f2e/README.yaml @@ -25,8 +25,9 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 336POPE_15254SOL_310K_v1 SOFTWARE_VERSION: 5.0.6 FF: CHARMM36-UA -FF_SOURCE: starting structure was made by reverse mapping an equilibrated MARTINI - POPE bilayer (constructed with the INSANE script) +FF_SOURCE: >- + starting structure was made by reverse mapping an equilibrated MARTINI POPE bilayer (constructed + with the INSANE script) FF_DATE: null CPT: null LOG: null diff --git a/Simulations/2e9/c2b/2e9c2b5fcf3b5504ff9fd97c893d20081f72a5fc/71f038f911d296a0407c424def4d6d6a6c69ea6c/README.yaml b/Simulations/2e9/c2b/2e9c2b5fcf3b5504ff9fd97c893d20081f72a5fc/71f038f911d296a0407c424def4d6d6a6c69ea6c/README.yaml index 0ae00b42dd..4d41a0932b 100644 --- a/Simulations/2e9/c2b/2e9c2b5fcf3b5504ff9fd97c893d20081f72a5fc/71f038f911d296a0407c424def4d6d6a6c69ea6c/README.yaml +++ b/Simulations/2e9/c2b/2e9c2b5fcf3b5504ff9fd97c893d20081f72a5fc/71f038f911d296a0407c424def4d6d6a6c69ea6c/README.yaml @@ -26,8 +26,7 @@ CPT: TRJLENGTH: 500100.0 TRAJECTORY_SIZE: 338098544 SOFTWARE_VERSION: 5.0.4 -FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet - and water+ions) +FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) TOP: - - POPC_72_310K_rmcomm_leaflets_md.top PREEQTIME: 0 diff --git a/Simulations/36e/333/36e333d9de810fdc8d0009df0e755225f7645161/36e333d9de810fdc8d0009df0e755225f7645161/README.yaml b/Simulations/36e/333/36e333d9de810fdc8d0009df0e755225f7645161/36e333d9de810fdc8d0009df0e755225f7645161/README.yaml index 8ff73c01cd..a5c0402793 100644 --- a/Simulations/36e/333/36e333d9de810fdc8d0009df0e755225f7645161/36e333d9de810fdc8d0009df0e755225f7645161/README.yaml +++ b/Simulations/36e/333/36e333d9de810fdc8d0009df0e755225f7645161/36e333d9de810fdc8d0009df0e755225f7645161/README.yaml @@ -32,8 +32,7 @@ AUTHORS_CONTACT: Kav, Batuhan SYSTEM: DOPC_450mM_NaCl_at_303K_with_AMOEBA SOFTWARE_VERSION: v7.5.1 FF: AMOEBA -FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in - publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 +FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 FF_DATE: null TRAJECTORY_SIZE: 1491950600 TRJLENGTH: 218400.0 diff --git a/Simulations/372/a91/372a917a2f528473eef642569a4c4f5f7472d473/e23ae04f10840187c2cf50c92451226d6bbadf63/README.yaml b/Simulations/372/a91/372a917a2f528473eef642569a4c4f5f7472d473/e23ae04f10840187c2cf50c92451226d6bbadf63/README.yaml index 747a9f828e..086dd53b78 100644 --- a/Simulations/372/a91/372a917a2f528473eef642569a4c4f5f7472d473/e23ae04f10840187c2cf50c92451226d6bbadf63/README.yaml +++ b/Simulations/372/a91/372a917a2f528473eef642569a4c4f5f7472d473/e23ae04f10840187c2cf50c92451226d6bbadf63/README.yaml @@ -25,8 +25,9 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 128DOPE_4789SOL_271K_v2 SOFTWARE_VERSION: 4.0.7 FF: Berger-DOPE-2004 -FF_SOURCE: starting structure was converted from equilibrated DOPC membrane simulated - with GROMOS-CKP force field, https://pubs.acs.org/doi/abs/10.1021/jp0366926 +FF_SOURCE: >- + starting structure was converted from equilibrated DOPC membrane simulated with GROMOS-CKP force + field, https://pubs.acs.org/doi/abs/10.1021/jp0366926 FF_DATE: null CPT: null LOG: null diff --git a/Simulations/3bc/fec/3bcfec940cb844905331c500649f8163e739f3e6/018b3585ccf055e9087a4b50ce06a3d9e4515fcb/README.yaml b/Simulations/3bc/fec/3bcfec940cb844905331c500649f8163e739f3e6/018b3585ccf055e9087a4b50ce06a3d9e4515fcb/README.yaml index 29fcca5e97..9c2ee7b793 100644 --- a/Simulations/3bc/fec/3bcfec940cb844905331c500649f8163e739f3e6/018b3585ccf055e9087a4b50ce06a3d9e4515fcb/README.yaml +++ b/Simulations/3bc/fec/3bcfec940cb844905331c500649f8163e739f3e6/018b3585ccf055e9087a4b50ce06a3d9e4515fcb/README.yaml @@ -29,8 +29,7 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 128DOPS_4480SOL_128SOD_303K_v2 SOFTWARE_VERSION: null FF: Berger -FF_SOURCE: starting structure from the CHARMM-GUI with the appropriate hydrogen atoms - removed +FF_SOURCE: starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed FF_DATE: null CPT: null LOG: null diff --git a/Simulations/3d1/f82/3d1f825918b4a3fd2f2dc52ad9d6948a78773bd0/e269c2c27722ad263b0d0f883e62e28f60d1ed1a/README.yaml b/Simulations/3d1/f82/3d1f825918b4a3fd2f2dc52ad9d6948a78773bd0/e269c2c27722ad263b0d0f883e62e28f60d1ed1a/README.yaml index 7b87690f73..3479dbcb23 100644 --- a/Simulations/3d1/f82/3d1f825918b4a3fd2f2dc52ad9d6948a78773bd0/e269c2c27722ad263b0d0f883e62e28f60d1ed1a/README.yaml +++ b/Simulations/3d1/f82/3d1f825918b4a3fd2f2dc52ad9d6948a78773bd0/e269c2c27722ad263b0d0f883e62e28f60d1ed1a/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 22CHOL_200POPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/41a/fb0/41afb0b8c74214ba9397c556a8b42fb02431ff34/eac51afd286254d306ef2f48f7c232593b888e70/README.yaml b/Simulations/41a/fb0/41afb0b8c74214ba9397c556a8b42fb02431ff34/eac51afd286254d306ef2f48f7c232593b888e70/README.yaml index c6aec88af9..ca304ed820 100644 --- a/Simulations/41a/fb0/41afb0b8c74214ba9397c556a8b42fb02431ff34/eac51afd286254d306ef2f48f7c232593b888e70/README.yaml +++ b/Simulations/41a/fb0/41afb0b8c74214ba9397c556a8b42fb02431ff34/eac51afd286254d306ef2f48f7c232593b888e70/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 50CHOL_200POPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/4ad/86c/4ad86cb9b8971f9acb7697e534c919359c720f91/5021b8fd43b9f7147ed1d883c1ccc172da878160/README.yaml b/Simulations/4ad/86c/4ad86cb9b8971f9acb7697e534c919359c720f91/5021b8fd43b9f7147ed1d883c1ccc172da878160/README.yaml index 7ad607e02d..b06a84164e 100644 --- a/Simulations/4ad/86c/4ad86cb9b8971f9acb7697e534c919359c720f91/5021b8fd43b9f7147ed1d883c1ccc172da878160/README.yaml +++ b/Simulations/4ad/86c/4ad86cb9b8971f9acb7697e534c919359c720f91/5021b8fd43b9f7147ed1d883c1ccc172da878160/README.yaml @@ -1,5 +1,5 @@ -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; - Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; Thalmann, Fabrice FF_DATE: June 2015 SYSTEM: 212DPPC_29826SOL_358K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/4ba/6f1/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/README.yaml b/Simulations/4ba/6f1/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/README.yaml index dc9d9c61d6..3ada27ad84 100644 --- a/Simulations/4ba/6f1/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/README.yaml +++ b/Simulations/4ba/6f1/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/4ba6f1d4240b72a165d921ec0246b14167ceeb9e/README.yaml @@ -32,8 +32,7 @@ AUTHORS_CONTACT: Kav, Batuhan SYSTEM: DOPC_1000mM_NaCl_at_303K_with_AMOEBA SOFTWARE_VERSION: v7.5.1 FF: AMOEBA -FF_SOURCE: "OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in\n\ - publication https://doi.org/10.1021/jacs.0c02394, \noriginal parameters https://doi.org/10.1080/00268976.2018.1436201\n" +FF_SOURCE: "OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in\npublication https://doi.org/10.1021/jacs.0c02394, \noriginal parameters https://doi.org/10.1080/00268976.2018.1436201\n" FF_DATE: null TRAJECTORY_SIZE: 1380782904 TRJLENGTH: 201600.0 diff --git a/Simulations/4db/c54/4dbc5440f1defe65905225286b9b446aa37082ad/8f5313af34f02d15f819a0d0dc843a780af3da87/README.yaml b/Simulations/4db/c54/4dbc5440f1defe65905225286b9b446aa37082ad/8f5313af34f02d15f819a0d0dc843a780af3da87/README.yaml index 84ee75fc58..6353d9f8ff 100644 --- a/Simulations/4db/c54/4dbc5440f1defe65905225286b9b446aa37082ad/8f5313af34f02d15f819a0d0dc843a780af3da87/README.yaml +++ b/Simulations/4db/c54/4dbc5440f1defe65905225286b9b446aa37082ad/8f5313af34f02d15f819a0d0dc843a780af3da87/README.yaml @@ -26,8 +26,7 @@ CPT: TRJLENGTH: 500100.0 TRAJECTORY_SIZE: 303517108 SOFTWARE_VERSION: 5.0.4 -FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet - and water+ions) +FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) TOP: - - POPC_72_310K_rmcomm_leaflets_low_hydration_md.top PREEQTIME: 0 diff --git a/Simulations/539/765/5397656665e3e09c0a7c7d74bc10a0d5cee6c6e5/60c6a7e3acf926f35aa7223b6defe9763bde0140/README.yaml b/Simulations/539/765/5397656665e3e09c0a7c7d74bc10a0d5cee6c6e5/60c6a7e3acf926f35aa7223b6defe9763bde0140/README.yaml index 9acd321117..d3685f5179 100644 --- a/Simulations/539/765/5397656665e3e09c0a7c7d74bc10a0d5cee6c6e5/60c6a7e3acf926f35aa7223b6defe9763bde0140/README.yaml +++ b/Simulations/539/765/5397656665e3e09c0a7c7d74bc10a0d5cee6c6e5/60c6a7e3acf926f35aa7223b6defe9763bde0140/README.yaml @@ -25,8 +25,9 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 128DOPE_4789SOL_271K_v1 SOFTWARE_VERSION: 4.0.7 FF: Berger-DOPE-2018 -FF_SOURCE: starting structure was converted from equilibrated DOPC membrane simulated - with GROMOS-CKP force field, https://pubs.acs.org/doi/abs/10.1021/jp0366926 +FF_SOURCE: >- + starting structure was converted from equilibrated DOPC membrane simulated with GROMOS-CKP force + field, https://pubs.acs.org/doi/abs/10.1021/jp0366926 FF_DATE: null CPT: null LOG: null diff --git a/Simulations/541/330/5413300b630cb69d17ee32f37bd904621cc091ec/3ef4a4a56814d7c1d1ed6dedb78cfb21d63e98f1/README.yaml b/Simulations/541/330/5413300b630cb69d17ee32f37bd904621cc091ec/3ef4a4a56814d7c1d1ed6dedb78cfb21d63e98f1/README.yaml index 29fa0398ba..b31d96cd1a 100644 --- a/Simulations/541/330/5413300b630cb69d17ee32f37bd904621cc091ec/3ef4a4a56814d7c1d1ed6dedb78cfb21d63e98f1/README.yaml +++ b/Simulations/541/330/5413300b630cb69d17ee32f37bd904621cc091ec/3ef4a4a56814d7c1d1ed6dedb78cfb21d63e98f1/README.yaml @@ -32,8 +32,7 @@ LOG: null TOP: - - topol.top WARNINGS: - FF: Hybrid force field test for fun, not production-ready. Simulated with Slipids - mdp. + FF: Hybrid force field test for fun, not production-ready. Simulated with Slipids mdp. TRAJECTORY_SIZE: 673355092 TRJLENGTH: 500100.0 TEMPERATURE: 298.0 diff --git a/Simulations/562/3a4/5623a4321f64219cfae8f12ec127db17406519a5/44e83a419d30e168df92735a26b23caeac357178/README.yaml b/Simulations/562/3a4/5623a4321f64219cfae8f12ec127db17406519a5/44e83a419d30e168df92735a26b23caeac357178/README.yaml index 041bc582ef..a4dbb8167d 100644 --- a/Simulations/562/3a4/5623a4321f64219cfae8f12ec127db17406519a5/44e83a419d30e168df92735a26b23caeac357178/README.yaml +++ b/Simulations/562/3a4/5623a4321f64219cfae8f12ec127db17406519a5/44e83a419d30e168df92735a26b23caeac357178/README.yaml @@ -143,3 +143,7 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-22' +EXPERIMENT: + ORDERPARAMETER: + DPPC: [] + FORMFACTOR: [] diff --git a/Simulations/56c/4ef/56c4ef96aa5c69d83e29931530671e25d8f6c700/b5c8e3f2998e01392bea661eea88bebed3439913/README.yaml b/Simulations/56c/4ef/56c4ef96aa5c69d83e29931530671e25d8f6c700/b5c8e3f2998e01392bea661eea88bebed3439913/README.yaml index 23f527ebd8..4cbca9acae 100644 --- a/Simulations/56c/4ef/56c4ef96aa5c69d83e29931530671e25d8f6c700/b5c8e3f2998e01392bea661eea88bebed3439913/README.yaml +++ b/Simulations/56c/4ef/56c4ef96aa5c69d83e29931530671e25d8f6c700/b5c8e3f2998e01392bea661eea88bebed3439913/README.yaml @@ -9,8 +9,9 @@ PREEQTIME: 0 TIMELEFTOUT: 1000 TEMPERATURE: 310.0 SYSTEM: POPC:Gb3_run2(95:5 mol:mol) -AUTHORS_CONTACT: Alexander Vogel (alexander.vogel@medizin.uni-leipzig.de), Daniel - B. Werz (daniel.werz@chemie.uni-freiburg.de) +AUTHORS_CONTACT: >- + Alexander Vogel (alexander.vogel@medizin.uni-leipzig.de), Daniel B. Werz + (daniel.werz@chemie.uni-freiburg.de) SOFTWARE_VERSION: 2019.4/2020 FF: CHARMM36m FF_SOURCE: CHARMM-GUI diff --git a/Simulations/575/abb/575abbac27d285e5cd72dd30f79c53c89a2e383c/f4cae31a4921bccd6e8ede49f15861d2bba0f7a1/README.yaml b/Simulations/575/abb/575abbac27d285e5cd72dd30f79c53c89a2e383c/f4cae31a4921bccd6e8ede49f15861d2bba0f7a1/README.yaml index 4d5f877ff9..aa4cc47840 100644 --- a/Simulations/575/abb/575abbac27d285e5cd72dd30f79c53c89a2e383c/f4cae31a4921bccd6e8ede49f15861d2bba0f7a1/README.yaml +++ b/Simulations/575/abb/575abbac27d285e5cd72dd30f79c53c89a2e383c/f4cae31a4921bccd6e8ede49f15861d2bba0f7a1/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_73CAL_146CLA_350K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/5b5/593/5b55930ae87dfb632f26c4c38a7a66080e7cbb7d/461d64647820187739173ba9094a030f7d5532c2/README.yaml b/Simulations/5b5/593/5b55930ae87dfb632f26c4c38a7a66080e7cbb7d/461d64647820187739173ba9094a030f7d5532c2/README.yaml index ea53c7349f..58c5b13e70 100644 --- a/Simulations/5b5/593/5b55930ae87dfb632f26c4c38a7a66080e7cbb7d/461d64647820187739173ba9094a030f7d5532c2/README.yaml +++ b/Simulations/5b5/593/5b55930ae87dfb632f26c4c38a7a66080e7cbb7d/461d64647820187739173ba9094a030f7d5532c2/README.yaml @@ -1,5 +1,5 @@ -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; - Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; Thalmann, Fabrice FF_DATE: June 2015 SYSTEM: 212DPPC_29826SOL_308K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/604/eca/604eca7a89f7875f3edf9b2f944f64cdcedcee37/ddb1026383c836b4d961a8dafc4c640823e9ba38/README.yaml b/Simulations/604/eca/604eca7a89f7875f3edf9b2f944f64cdcedcee37/ddb1026383c836b4d961a8dafc4c640823e9ba38/README.yaml index 9d740a111a..4505795244 100644 --- a/Simulations/604/eca/604eca7a89f7875f3edf9b2f944f64cdcedcee37/ddb1026383c836b4d961a8dafc4c640823e9ba38/README.yaml +++ b/Simulations/604/eca/604eca7a89f7875f3edf9b2f944f64cdcedcee37/ddb1026383c836b4d961a8dafc4c640823e9ba38/README.yaml @@ -25,8 +25,9 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 128POPE_3552SOL_303K_v2 SOFTWARE_VERSION: 4.0.7 FF: Berger-POPE-2004 -FF_SOURCE: starting structure from equilibrated POPE membrane simulated with the GROMOS-CKP - force field, PE parameters https://pubs.acs.org/doi/abs/10.1021/jp0366926 +FF_SOURCE: >- + starting structure from equilibrated POPE membrane simulated with the GROMOS-CKP force field, PE + parameters https://pubs.acs.org/doi/abs/10.1021/jp0366926 FF_DATE: null CPT: null LOG: null diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_FragmentQuality.json b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..db2c9004a4 --- /dev/null +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6571, "total": 0.6571} \ No newline at end of file diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_OrderParameters_quality.json b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..e29adbc26c --- /dev/null +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": NaN, + "M_G1C13_M M_G1C13H2_M": NaN, + "M_G1C14_M M_G1C14H1_M": NaN, + "M_G1C14_M M_G1C14H2_M": NaN, + "M_G1C15_M M_G1C15H1_M": NaN, + "M_G1C15_M M_G1C15H2_M": NaN, + "M_G1C16_M M_G1C16H1_M": NaN, + "M_G1C16_M M_G1C16H2_M": NaN, + "M_G1C17_M M_G1C17H1_M": NaN, + "M_G1C17_M M_G1C17H2_M": NaN, + "M_G1C17_M M_G1C17H3_M": NaN, + "M_G1C3_M M_G1C3H1_M": NaN, + "M_G1C3_M M_G1C3H2_M": NaN, + "M_G1C4_M M_G1C4H1_M": NaN, + "M_G1C4_M M_G1C4H2_M": NaN, + "M_G1C5_M M_G1C5H1_M": NaN, + "M_G1C5_M M_G1C5H2_M": NaN, + "M_G1C6_M M_G1C6H1_M": NaN, + "M_G1C6_M M_G1C6H2_M": NaN, + "M_G1C7_M M_G1C7H1_M": NaN, + "M_G1C7_M M_G1C7H2_M": NaN, + "M_G1C8_M M_G1C8H1_M": NaN, + "M_G1C8_M M_G1C8H2_M": NaN, + "M_G1C9_M M_G1C9H1_M": NaN, + "M_G1C9_M M_G1C9H2_M": NaN, + "M_G1_M M_G1H1_M": NaN, + "M_G1_M M_G1H2_M": NaN, + "M_G2C10_M M_G2C10H1_M": NaN, + "M_G2C10_M M_G2C10H2_M": NaN, + "M_G2C11_M M_G2C11H1_M": NaN, + "M_G2C11_M M_G2C11H2_M": NaN, + "M_G2C12_M M_G2C12H1_M": NaN, + "M_G2C12_M M_G2C12H2_M": NaN, + "M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.0304, + "M_G3C4_M M_G3C4H2_M": 0.0278, + "M_G3C5_M M_G3C5H1_M": 0.927, + "M_G3C5_M M_G3C5H2_M": 0.9145, + "M_G3N6C1_M M_G3N6C1H1_M": 0.9878, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9872, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9877, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9879, + "M_G3N6C2_M M_G3N6C2H2_M": 0.9887, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9883, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9878, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9878, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9887, + "M_G3_M M_G3H1_M": 0.1171, + "M_G3_M M_G3H2_M": 0.9192 + } +} \ No newline at end of file diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/FormFactorQuality.json b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/FormFactorQuality.json new file mode 100644 index 0000000000..75509d3985 --- /dev/null +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/FormFactorQuality.json @@ -0,0 +1 @@ +[0.1789, 83.3434] \ No newline at end of file diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/README.yaml b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/README.yaml index 58ef93af16..a9ba62e4dd 100644 --- a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/README.yaml +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/README.yaml @@ -143,3 +143,9 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-23' +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/SYSTEM_quality.json b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/SYSTEM_quality.json new file mode 100644 index 0000000000..53c6c61a5e --- /dev/null +++ b/Simulations/627/f10/627f109a3f0966dd1ac26074c08e55dbf30dc1c3/90ae66b30e033c08b8f754a4a93053086913586e/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6571, "tails": 0.0, "total": 0.6571} \ No newline at end of file diff --git a/Simulations/63a/479/63a47940524010d5a2ff46f0d4c89b4b69e0ad4f/9d9ca60b644e801ec759177e4b1cbe5bf413fe25/README.yaml b/Simulations/63a/479/63a47940524010d5a2ff46f0d4c89b4b69e0ad4f/9d9ca60b644e801ec759177e4b1cbe5bf413fe25/README.yaml index ebbf533707..3717ae92e7 100644 --- a/Simulations/63a/479/63a47940524010d5a2ff46f0d4c89b4b69e0ad4f/9d9ca60b644e801ec759177e4b1cbe5bf413fe25/README.yaml +++ b/Simulations/63a/479/63a47940524010d5a2ff46f0d4c89b4b69e0ad4f/9d9ca60b644e801ec759177e4b1cbe5bf413fe25/README.yaml @@ -23,8 +23,9 @@ AUTHORS_CONTACT: Milan Rodriguez, Paula; Fuchs, Patrick F.J. SYSTEM: 128POPC_5120SOL_300K SOFTWARE_VERSION: null FF: MacRog -FF_SOURCE: starting structure from CHARMM-GUI, the initial PDB file was modified to - match MacRog nomenclature and atom order +FF_SOURCE: >- + starting structure from CHARMM-GUI, the initial PDB file was modified to match MacRog nomenclature + and atom order FF_DATE: null CPT: null LOG: null diff --git a/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/667f6c5e4750b15b516a68c3a85dab4c6d2e03fd/README.yaml b/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/667f6c5e4750b15b516a68c3a85dab4c6d2e03fd/README.yaml index 506047d7c7..92abd167af 100644 --- a/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/667f6c5e4750b15b516a68c3a85dab4c6d2e03fd/README.yaml +++ b/Simulations/64f/277/64f27772e410f8ae052ec6976cd430718ae476f6/667f6c5e4750b15b516a68c3a85dab4c6d2e03fd/README.yaml @@ -1,5 +1,4 @@ -AUTHORS_CONTACT: Martinez-Seara, Hector; Javanainen, Matti; Rissanen, Sami; Lolicato, - Fabio +AUTHORS_CONTACT: Martinez-Seara, Hector; Javanainen, Matti; Rissanen, Sami; Lolicato, Fabio FF_DATE: null SYSTEM: 512DPPC_20480SOL_55SOD_55CLA_320K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/207dcbf19b201fbe39855937864886eae03e2dac/README.yaml b/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/207dcbf19b201fbe39855937864886eae03e2dac/README.yaml index 2a3d53b092..5bb3b1beb0 100644 --- a/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/207dcbf19b201fbe39855937864886eae03e2dac/README.yaml +++ b/Simulations/66b/22e/66b22ee83575dcbca5a36163c773cc4d93534418/207dcbf19b201fbe39855937864886eae03e2dac/README.yaml @@ -1,5 +1,4 @@ -AUTHORS_CONTACT: Martinez-Seara, Hector; Javanainen, Matti; Rissanen, Sami; Lolicato, - Fabio +AUTHORS_CONTACT: Martinez-Seara, Hector; Javanainen, Matti; Rissanen, Sami; Lolicato, Fabio FF_DATE: null SYSTEM: 512DPPC_20480SOL_55SOD_55CLA_320K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_FragmentQuality.json b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..dc5205e894 --- /dev/null +++ b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6118, "total": 0.6118} \ No newline at end of file diff --git a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_OrderParameters_quality.json b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..de3c72b8b3 --- /dev/null +++ b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": NaN, + "M_G1C13_M M_G1C13H2_M": NaN, + "M_G1C14_M M_G1C14H1_M": NaN, + "M_G1C14_M M_G1C14H2_M": NaN, + "M_G1C15_M M_G1C15H1_M": NaN, + "M_G1C15_M M_G1C15H2_M": NaN, + "M_G1C16_M M_G1C16H1_M": NaN, + "M_G1C16_M M_G1C16H2_M": NaN, + "M_G1C17_M M_G1C17H1_M": NaN, + "M_G1C17_M M_G1C17H2_M": NaN, + "M_G1C17_M M_G1C17H3_M": NaN, + "M_G1C3_M M_G1C3H1_M": NaN, + "M_G1C3_M M_G1C3H2_M": NaN, + "M_G1C4_M M_G1C4H1_M": NaN, + "M_G1C4_M M_G1C4H2_M": NaN, + "M_G1C5_M M_G1C5H1_M": NaN, + "M_G1C5_M M_G1C5H2_M": NaN, + "M_G1C6_M M_G1C6H1_M": NaN, + "M_G1C6_M M_G1C6H2_M": NaN, + "M_G1C7_M M_G1C7H1_M": NaN, + "M_G1C7_M M_G1C7H2_M": NaN, + "M_G1C8_M M_G1C8H1_M": NaN, + "M_G1C8_M M_G1C8H2_M": NaN, + "M_G1C9_M M_G1C9H1_M": NaN, + "M_G1C9_M M_G1C9H2_M": NaN, + "M_G1_M M_G1H1_M": NaN, + "M_G1_M M_G1H2_M": NaN, + "M_G2C10_M M_G2C10H1_M": NaN, + "M_G2C10_M M_G2C10H2_M": NaN, + "M_G2C11_M M_G2C11H1_M": NaN, + "M_G2C11_M M_G2C11H2_M": NaN, + "M_G2C12_M M_G2C12H1_M": NaN, + "M_G2C12_M M_G2C12H2_M": NaN, + "M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.083, + "M_G3C4_M M_G3C4H2_M": 0.0737, + "M_G3C5_M M_G3C5H1_M": 0.4601, + "M_G3C5_M M_G3C5H2_M": 0.3097, + "M_G3N6C1_M M_G3N6C1H1_M": 0.9851, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9864, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9871, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9857, + "M_G3N6C2_M M_G3N6C2H2_M": 0.9869, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9856, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9859, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9858, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9868, + "M_G3_M M_G3H1_M": 0.7344, + "M_G3_M M_G3H2_M": 0.4768 + } +} \ No newline at end of file diff --git a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/README.yaml b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/README.yaml index 2c5006ecea..582d758fc6 100644 --- a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/README.yaml +++ b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/README.yaml @@ -143,3 +143,8 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-23' +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: [] diff --git a/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/SYSTEM_quality.json b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/SYSTEM_quality.json new file mode 100644 index 0000000000..fe09aab50b --- /dev/null +++ b/Simulations/670/484/6704849a21596a96b4e490419f3c937d719b2904/718296d4c5b00da31a47037e847ab0d5c5246d2c/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6118, "tails": 0.0, "total": 0.6118} \ No newline at end of file diff --git a/Simulations/6df/e30/6dfe305837741f64feb89bba6ef9ae287cc69f03/5d840adb19c0153ec71e54f1dc918259bbcc6e6f/README.yaml b/Simulations/6df/e30/6dfe305837741f64feb89bba6ef9ae287cc69f03/5d840adb19c0153ec71e54f1dc918259bbcc6e6f/README.yaml index c4403fadbf..e9ca6c5837 100644 --- a/Simulations/6df/e30/6dfe305837741f64feb89bba6ef9ae287cc69f03/5d840adb19c0153ec71e54f1dc918259bbcc6e6f/README.yaml +++ b/Simulations/6df/e30/6dfe305837741f64feb89bba6ef9ae287cc69f03/5d840adb19c0153ec71e54f1dc918259bbcc6e6f/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 50CHOL_200POPC_9000SOL_73CAL_146CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/671c42892cc90cc0e315085e3fd9e12bb9318ed0/README.yaml b/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/671c42892cc90cc0e315085e3fd9e12bb9318ed0/README.yaml index ab171bc05f..c3d01687da 100644 --- a/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/671c42892cc90cc0e315085e3fd9e12bb9318ed0/README.yaml +++ b/Simulations/722/744/7227444b737b8023a50556d24a364903f2fee400/671c42892cc90cc0e315085e3fd9e12bb9318ed0/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/72d/1bb/72d1bb7141ef2d9b6f447cefc2c410e82bd8bdb9/14e3a78527c746635c4c6e4861050bf7eab0430a/README.yaml b/Simulations/72d/1bb/72d1bb7141ef2d9b6f447cefc2c410e82bd8bdb9/14e3a78527c746635c4c6e4861050bf7eab0430a/README.yaml index c94a0cd8d5..aee847972f 100644 --- a/Simulations/72d/1bb/72d1bb7141ef2d9b6f447cefc2c410e82bd8bdb9/14e3a78527c746635c4c6e4861050bf7eab0430a/README.yaml +++ b/Simulations/72d/1bb/72d1bb7141ef2d9b6f447cefc2c410e82bd8bdb9/14e3a78527c746635c4c6e4861050bf7eab0430a/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 86CHOL_200POPC_9000SOL_73CAL_146CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/745/bad/745bad0b0de2ec73e911515d768eeaa840003d1c/2550786d5679f11478db96c5a06a506c22ca4b1a/README.yaml b/Simulations/745/bad/745bad0b0de2ec73e911515d768eeaa840003d1c/2550786d5679f11478db96c5a06a506c22ca4b1a/README.yaml index ab44e1c58e..c7491aebe5 100644 --- a/Simulations/745/bad/745bad0b0de2ec73e911515d768eeaa840003d1c/2550786d5679f11478db96c5a06a506c22ca4b1a/README.yaml +++ b/Simulations/745/bad/745bad0b0de2ec73e911515d768eeaa840003d1c/2550786d5679f11478db96c5a06a506c22ca4b1a/README.yaml @@ -1,5 +1,5 @@ -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; - Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; Thalmann, Fabrice FF_DATE: June 2015 SYSTEM: 212DPPC_29826SOL_338K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/7cf/9df/7cf9df0cc6fe319d93e3f5635b2c6b517513cbf5/b1e8bdfc572caaf640f503bff2726ed0a1a793a3/README.yaml b/Simulations/7cf/9df/7cf9df0cc6fe319d93e3f5635b2c6b517513cbf5/b1e8bdfc572caaf640f503bff2726ed0a1a793a3/README.yaml index 62b2f34a1d..fb64ad135d 100644 --- a/Simulations/7cf/9df/7cf9df0cc6fe319d93e3f5635b2c6b517513cbf5/b1e8bdfc572caaf640f503bff2726ed0a1a793a3/README.yaml +++ b/Simulations/7cf/9df/7cf9df0cc6fe319d93e3f5635b2c6b517513cbf5/b1e8bdfc572caaf640f503bff2726ed0a1a793a3/README.yaml @@ -27,8 +27,7 @@ CPT: TRJLENGTH: 500100.0 TRAJECTORY_SIZE: 303543904 SOFTWARE_VERSION: 5.0.4 -FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet - and water+ions) +FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) TOP: - - POPC_72_303K_rmcomm_leaflets_low_hydration_md.top PREEQTIME: 0 diff --git a/Simulations/803/9d5/8039d537f1f2143d20248b72c9b87d81dbb4cd41/8039d537f1f2143d20248b72c9b87d81dbb4cd41/README.yaml b/Simulations/803/9d5/8039d537f1f2143d20248b72c9b87d81dbb4cd41/8039d537f1f2143d20248b72c9b87d81dbb4cd41/README.yaml index d2af0cf51d..fbb2558dc8 100644 --- a/Simulations/803/9d5/8039d537f1f2143d20248b72c9b87d81dbb4cd41/8039d537f1f2143d20248b72c9b87d81dbb4cd41/README.yaml +++ b/Simulations/803/9d5/8039d537f1f2143d20248b72c9b87d81dbb4cd41/8039d537f1f2143d20248b72c9b87d81dbb4cd41/README.yaml @@ -32,8 +32,7 @@ AUTHORS_CONTACT: Kav, Batuhan SYSTEM: DOPC_450mM_CaCl2_at_303K_with_AMOEBA SOFTWARE_VERSION: v7.5.1 FF: AMOEBA -FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in - publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 +FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 FF_DATE: null TRAJECTORY_SIZE: 1493479544 TRJLENGTH: 218400.0 diff --git a/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/45b6ab86e2a313b1be49ac29d8edb6b3688a0421/README.yaml b/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/45b6ab86e2a313b1be49ac29d8edb6b3688a0421/README.yaml index 14fb56c4b0..daa98ea26e 100644 --- a/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/45b6ab86e2a313b1be49ac29d8edb6b3688a0421/README.yaml +++ b/Simulations/82e/424/82e42412f1383f19441f90baf20721ab773ce1fa/45b6ab86e2a313b1be49ac29d8edb6b3688a0421/README.yaml @@ -9,8 +9,9 @@ PREEQTIME: 0 TIMELEFTOUT: 1000 TEMPERATURE: 310.0 SYSTEM: POPC:Gb3_run1(95:5 mol:mol) -AUTHORS_CONTACT: Alexander Vogel (alexander.vogel@medizin.uni-leipzig.de), Daniel - B. Werz (daniel.werz@chemie.uni-freiburg.de) +AUTHORS_CONTACT: >- + Alexander Vogel (alexander.vogel@medizin.uni-leipzig.de), Daniel B. Werz + (daniel.werz@chemie.uni-freiburg.de) SOFTWARE_VERSION: 2019.4/2020 FF: CHARMM36m FF_SOURCE: CHARMM-GUI diff --git a/Simulations/8b4/def/8b4defac09883665a8c2e32302d5080664fc77aa/f0b754bfeb545d99e3d319216c6894adbf27fee2/README.yaml b/Simulations/8b4/def/8b4defac09883665a8c2e32302d5080664fc77aa/f0b754bfeb545d99e3d319216c6894adbf27fee2/README.yaml index 9aafb9b727..df238fe606 100644 --- a/Simulations/8b4/def/8b4defac09883665a8c2e32302d5080664fc77aa/f0b754bfeb545d99e3d319216c6894adbf27fee2/README.yaml +++ b/Simulations/8b4/def/8b4defac09883665a8c2e32302d5080664fc77aa/f0b754bfeb545d99e3d319216c6894adbf27fee2/README.yaml @@ -27,8 +27,7 @@ CPT: TRJLENGTH: 500100.0 TRAJECTORY_SIZE: 294825836 SOFTWARE_VERSION: 5.0.4 -FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet - and water+ions) +FF: CHARMM36 (center of mass removed independently for upper leaflet, lower leaflet and water+ions) TOP: - - DPPC_72_325K_rmcomm_leaflets_low_hydration_md.top PREEQTIME: 0 diff --git a/Simulations/8ce/23b/8ce23bb33af41c05a6f9e78ee540b0f0b3d80b61/8e30fa47b8446f2eb523b55d501f6c6ea6e39675/README.yaml b/Simulations/8ce/23b/8ce23bb33af41c05a6f9e78ee540b0f0b3d80b61/8e30fa47b8446f2eb523b55d501f6c6ea6e39675/README.yaml index c851239ec4..e59f682c49 100644 --- a/Simulations/8ce/23b/8ce23bb33af41c05a6f9e78ee540b0f0b3d80b61/8e30fa47b8446f2eb523b55d501f6c6ea6e39675/README.yaml +++ b/Simulations/8ce/23b/8ce23bb33af41c05a6f9e78ee540b0f0b3d80b61/8e30fa47b8446f2eb523b55d501f6c6ea6e39675/README.yaml @@ -1,5 +1,5 @@ -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; - Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; Thalmann, Fabrice FF_DATE: June 2015 SYSTEM: 212DPPC_29826SOL_348K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/8ea/f33/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/README.yaml b/Simulations/8ea/f33/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/README.yaml index b470e85199..7be8127dc8 100644 --- a/Simulations/8ea/f33/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/README.yaml +++ b/Simulations/8ea/f33/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/8eaf33ff270a3ffb78a6a2cb66dcf0e39a7b6eeb/README.yaml @@ -31,8 +31,7 @@ AUTHORS_CONTACT: Kav, Batuhan SYSTEM: DOPC_1000mM_CaCl2_at_303K_with_AMOEBA SOFTWARE_VERSION: v7.5.1 FF: AMOEBA -FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in - publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 +FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 FF_DATE: null TRAJECTORY_SIZE: 1499986540 TRJLENGTH: 218400.0 diff --git a/Simulations/903/468/90346863c8dd3626b433c9f51d06c7d4a263db00/44e1a30df49fd6fafdaa7c1fdeba9a1e215645ad/README.yaml b/Simulations/903/468/90346863c8dd3626b433c9f51d06c7d4a263db00/44e1a30df49fd6fafdaa7c1fdeba9a1e215645ad/README.yaml index 051872d3a7..c229064133 100644 --- a/Simulations/903/468/90346863c8dd3626b433c9f51d06c7d4a263db00/44e1a30df49fd6fafdaa7c1fdeba9a1e215645ad/README.yaml +++ b/Simulations/903/468/90346863c8dd3626b433c9f51d06c7d4a263db00/44e1a30df49fd6fafdaa7c1fdeba9a1e215645ad/README.yaml @@ -1,5 +1,5 @@ -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; - Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; Thalmann, Fabrice FF_DATE: June 2015 SYSTEM: 212DPPC_29826SOL_328K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/924/ea6/924ea67948ef064e85991f142a5e2388af6296b4/c2626917d469d7e2818613569ed95c834174c82c/README.yaml b/Simulations/924/ea6/924ea67948ef064e85991f142a5e2388af6296b4/c2626917d469d7e2818613569ed95c834174c82c/README.yaml index 598ec63982..72f398f2f3 100644 --- a/Simulations/924/ea6/924ea67948ef064e85991f142a5e2388af6296b4/c2626917d469d7e2818613569ed95c834174c82c/README.yaml +++ b/Simulations/924/ea6/924ea67948ef064e85991f142a5e2388af6296b4/c2626917d469d7e2818613569ed95c834174c82c/README.yaml @@ -24,8 +24,9 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 128DOPE_4789SOL_271K_v1 SOFTWARE_VERSION: 4.0.7 FF: Berger-DOPE-2004 -FF_SOURCE: starting structure was converted from equilibrated DOPC membrane simulated - with GROMOS-CKP force field, https://pubs.acs.org/doi/abs/10.1021/jp0366926 +FF_SOURCE: >- + starting structure was converted from equilibrated DOPC membrane simulated with GROMOS-CKP force + field, https://pubs.acs.org/doi/abs/10.1021/jp0366926 FF_DATE: null CPT: null LOG: null diff --git a/Simulations/92b/b78/92bb78fa030c101f9a684e523e010dc1f1358a9e/56ef975f609cc342145b12c14ac8b68079849c00/README.yaml b/Simulations/92b/b78/92bb78fa030c101f9a684e523e010dc1f1358a9e/56ef975f609cc342145b12c14ac8b68079849c00/README.yaml index faf6eea3ab..2c460c343b 100644 --- a/Simulations/92b/b78/92bb78fa030c101f9a684e523e010dc1f1358a9e/56ef975f609cc342145b12c14ac8b68079849c00/README.yaml +++ b/Simulations/92b/b78/92bb78fa030c101f9a684e523e010dc1f1358a9e/56ef975f609cc342145b12c14ac8b68079849c00/README.yaml @@ -22,8 +22,9 @@ AUTHORS_CONTACT: Milan Rodriguez, Paula; Fuchs, Patrick F.J. SYSTEM: 128POPE_5120SOL_300K SOFTWARE_VERSION: null FF: MacRog -FF_SOURCE: starting structure from CHARMM-GUI, the initial PDB file was modified to - match MacRog nomenclature and atom order +FF_SOURCE: >- + starting structure from CHARMM-GUI, the initial PDB file was modified to match MacRog nomenclature + and atom order FF_DATE: null CPT: null LOG: null diff --git a/Simulations/92f/99b/92f99b3fdbed01824af994eeb0b4bd62529784ab/92f99b3fdbed01824af994eeb0b4bd62529784ab/README.yaml b/Simulations/92f/99b/92f99b3fdbed01824af994eeb0b4bd62529784ab/92f99b3fdbed01824af994eeb0b4bd62529784ab/README.yaml index 834d9803d1..4aab882ec0 100644 --- a/Simulations/92f/99b/92f99b3fdbed01824af994eeb0b4bd62529784ab/92f99b3fdbed01824af994eeb0b4bd62529784ab/README.yaml +++ b/Simulations/92f/99b/92f99b3fdbed01824af994eeb0b4bd62529784ab/92f99b3fdbed01824af994eeb0b4bd62529784ab/README.yaml @@ -23,8 +23,7 @@ AUTHORS_CONTACT: Kav, Batuhan SYSTEM: POPE_nosalt_at_303K_with_AMOEBA SOFTWARE_VERSION: v7.5.1 FF: AMOEBA -FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in - publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 +FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 FF_DATE: null TRAJECTORY_SIZE: 1976959348 TRJLENGTH: 305940.0 diff --git a/Simulations/9a1/605/9a16054f3de88c6236c869a48b7ba22a4560c031/1ee911c0a7597ddccc6a2f88e6de0103731df881/README.yaml b/Simulations/9a1/605/9a16054f3de88c6236c869a48b7ba22a4560c031/1ee911c0a7597ddccc6a2f88e6de0103731df881/README.yaml index 137a8630f3..ae8f10a2ab 100644 --- a/Simulations/9a1/605/9a16054f3de88c6236c869a48b7ba22a4560c031/1ee911c0a7597ddccc6a2f88e6de0103731df881/README.yaml +++ b/Simulations/9a1/605/9a16054f3de88c6236c869a48b7ba22a4560c031/1ee911c0a7597ddccc6a2f88e6de0103731df881/README.yaml @@ -31,8 +31,9 @@ AUTHORS_CONTACT: Ollila O. H. Samuli; Ferreira Tiago; Topgaard Daniel SYSTEM: 78CHOL_50POPC_5782SOL_298K_Berger SOFTWARE_VERSION: 4.5 FF: Berger and Modified Höltje model for cholesterol -FF_SOURCE: http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X - for cholesterol +FF_SOURCE: >- + http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X for + cholesterol FF_DATE: null CPT: null LOG: null diff --git a/Simulations/9cc/a43/9cca43b014e94e814ad67fa24422986dd1effb72/93cad0b1b10eb15dc60d41489a6821f40ee4cb69/README.yaml b/Simulations/9cc/a43/9cca43b014e94e814ad67fa24422986dd1effb72/93cad0b1b10eb15dc60d41489a6821f40ee4cb69/README.yaml index 4bef9fcfdb..1468059c04 100644 --- a/Simulations/9cc/a43/9cca43b014e94e814ad67fa24422986dd1effb72/93cad0b1b10eb15dc60d41489a6821f40ee4cb69/README.yaml +++ b/Simulations/9cc/a43/9cca43b014e94e814ad67fa24422986dd1effb72/93cad0b1b10eb15dc60d41489a6821f40ee4cb69/README.yaml @@ -143,3 +143,7 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-22' +EXPERIMENT: + ORDERPARAMETER: + DPPC: [] + FORMFACTOR: [] diff --git a/Simulations/9e5/d4e/9e5d4ec35e04867608e230e2425b609d3c26654b/fd5c1bd3057280a314e4d16762b768cfd683ff29/README.yaml b/Simulations/9e5/d4e/9e5d4ec35e04867608e230e2425b609d3c26654b/fd5c1bd3057280a314e4d16762b768cfd683ff29/README.yaml index 8eeefba752..6e4e4b6afb 100644 --- a/Simulations/9e5/d4e/9e5d4ec35e04867608e230e2425b609d3c26654b/fd5c1bd3057280a314e4d16762b768cfd683ff29/README.yaml +++ b/Simulations/9e5/d4e/9e5d4ec35e04867608e230e2425b609d3c26654b/fd5c1bd3057280a314e4d16762b768cfd683ff29/README.yaml @@ -35,8 +35,9 @@ AUTHORS_CONTACT: Ollila, Samuli; Khandelia, Himanshu SYSTEM: 90POPC_38PAzePCdeprot_7250SOL_38POT_298K SOFTWARE_VERSION: 4.5 FF: Berger -FF_SOURCE: H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 - – 2743, http://dx.doi.org/10.1016/j.bpj.2009.01.007 for PAzePCdeprot +FF_SOURCE: >- + H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 – 2743, + http://dx.doi.org/10.1016/j.bpj.2009.01.007 for PAzePCdeprot FF_DATE: null CPT: null LOG: null diff --git a/Simulations/a00/2c2/a002c28997069825fa42a6b751369d8062533e14/757216c36b032096aca0f434eba8799fcd5e3860/README.yaml b/Simulations/a00/2c2/a002c28997069825fa42a6b751369d8062533e14/757216c36b032096aca0f434eba8799fcd5e3860/README.yaml index 619bb79257..4e5194b84c 100644 --- a/Simulations/a00/2c2/a002c28997069825fa42a6b751369d8062533e14/757216c36b032096aca0f434eba8799fcd5e3860/README.yaml +++ b/Simulations/a00/2c2/a002c28997069825fa42a6b751369d8062533e14/757216c36b032096aca0f434eba8799fcd5e3860/README.yaml @@ -18,8 +18,9 @@ COMPOSITION: COUNT: 42642 MAPPING: mappingTIP3Pwater.yaml DIR_WRK: /usr/home/bort/Databank -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Gola, Adrien; Marques, Carlos; Benzerara, - Olivier; Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Gola, Adrien; Marques, Carlos; Benzerara, Olivier; Thalmann, + Fabrice SYSTEM: 256DPPC_42642SOL_288K SOFTWARE_VERSION: 2016.4 FF: CHARMM36 diff --git a/Simulations/a1d/1ce/a1d1ce26a05e41216af050e363e0540da9528ac3/4aad649cb6def78cf0a3a5cffdc7ab2ef1d81e8f/README.yaml b/Simulations/a1d/1ce/a1d1ce26a05e41216af050e363e0540da9528ac3/4aad649cb6def78cf0a3a5cffdc7ab2ef1d81e8f/README.yaml index 7367e38921..8c18e44d5a 100644 --- a/Simulations/a1d/1ce/a1d1ce26a05e41216af050e363e0540da9528ac3/4aad649cb6def78cf0a3a5cffdc7ab2ef1d81e8f/README.yaml +++ b/Simulations/a1d/1ce/a1d1ce26a05e41216af050e363e0540da9528ac3/4aad649cb6def78cf0a3a5cffdc7ab2ef1d81e8f/README.yaml @@ -11,8 +11,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_21SOD_21CLA_350K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/a3d/f66/a3df66f326ff40b301fc96f980adb9bcc461bfb4/8c090fc702f8a04415326dc3f24c96db04c72274/README.yaml b/Simulations/a3d/f66/a3df66f326ff40b301fc96f980adb9bcc461bfb4/8c090fc702f8a04415326dc3f24c96db04c72274/README.yaml index 51ae486066..f853800419 100644 --- a/Simulations/a3d/f66/a3df66f326ff40b301fc96f980adb9bcc461bfb4/8c090fc702f8a04415326dc3f24c96db04c72274/README.yaml +++ b/Simulations/a3d/f66/a3df66f326ff40b301fc96f980adb9bcc461bfb4/8c090fc702f8a04415326dc3f24c96db04c72274/README.yaml @@ -8,8 +8,9 @@ PREEQTIME: 100 TIMELEFTOUT: 0 TEMPERATURE: 342.0 SYSTEM: DPPE in TIP3(Water) at 342K -AUTHORS_CONTACT: Avneesh Singh - ms23249@iisermohali.ac.in, Anubhav Ganguly - ms23237@iisermohali.ac.in, - Prof. M. Miettinen Markus.Miettinen@uib.no +AUTHORS_CONTACT: >- + Avneesh Singh - ms23249@iisermohali.ac.in, Anubhav Ganguly - ms23237@iisermohali.ac.in, Prof. M. + Miettinen Markus.Miettinen@uib.no SOFTWARE_VERSION: '2023.3' FF: CHARMM36 FF_SOURCE: Charmm-GUI diff --git a/Simulations/a5b/236/a5b236bf329671e10e32c2fc798fb7a3a5136db6/57b957fbea76919f972a818e2f0de55363f89717/README.yaml b/Simulations/a5b/236/a5b236bf329671e10e32c2fc798fb7a3a5136db6/57b957fbea76919f972a818e2f0de55363f89717/README.yaml index 5f083a3b5a..7f2183a236 100644 --- a/Simulations/a5b/236/a5b236bf329671e10e32c2fc798fb7a3a5136db6/57b957fbea76919f972a818e2f0de55363f89717/README.yaml +++ b/Simulations/a5b/236/a5b236bf329671e10e32c2fc798fb7a3a5136db6/57b957fbea76919f972a818e2f0de55363f89717/README.yaml @@ -11,8 +11,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_21SOD_21CLA_330K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_FragmentQuality.json b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..3b2248a10c --- /dev/null +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6585, "total": 0.6585} \ No newline at end of file diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_OrderParameters_quality.json b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..c36dfedf79 --- /dev/null +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": NaN, + "M_G1C13_M M_G1C13H2_M": NaN, + "M_G1C14_M M_G1C14H1_M": NaN, + "M_G1C14_M M_G1C14H2_M": NaN, + "M_G1C15_M M_G1C15H1_M": NaN, + "M_G1C15_M M_G1C15H2_M": NaN, + "M_G1C16_M M_G1C16H1_M": NaN, + "M_G1C16_M M_G1C16H2_M": NaN, + "M_G1C17_M M_G1C17H1_M": NaN, + "M_G1C17_M M_G1C17H2_M": NaN, + "M_G1C17_M M_G1C17H3_M": NaN, + "M_G1C3_M M_G1C3H1_M": NaN, + "M_G1C3_M M_G1C3H2_M": NaN, + "M_G1C4_M M_G1C4H1_M": NaN, + "M_G1C4_M M_G1C4H2_M": NaN, + "M_G1C5_M M_G1C5H1_M": NaN, + "M_G1C5_M M_G1C5H2_M": NaN, + "M_G1C6_M M_G1C6H1_M": NaN, + "M_G1C6_M M_G1C6H2_M": NaN, + "M_G1C7_M M_G1C7H1_M": NaN, + "M_G1C7_M M_G1C7H2_M": NaN, + "M_G1C8_M M_G1C8H1_M": NaN, + "M_G1C8_M M_G1C8H2_M": NaN, + "M_G1C9_M M_G1C9H1_M": NaN, + "M_G1C9_M M_G1C9H2_M": NaN, + "M_G1_M M_G1H1_M": NaN, + "M_G1_M M_G1H2_M": NaN, + "M_G2C10_M M_G2C10H1_M": NaN, + "M_G2C10_M M_G2C10H2_M": NaN, + "M_G2C11_M M_G2C11H1_M": NaN, + "M_G2C11_M M_G2C11H2_M": NaN, + "M_G2C12_M M_G2C12H1_M": NaN, + "M_G2C12_M M_G2C12H2_M": NaN, + "M_G2C13_M M_G2C13H1_M": NaN, + "M_G2C13_M M_G2C13H2_M": NaN, + "M_G2C14_M M_G2C14H1_M": NaN, + "M_G2C14_M M_G2C14H2_M": NaN, + "M_G2C15_M M_G2C15H1_M": NaN, + "M_G2C15_M M_G2C15H2_M": NaN, + "M_G2C16_M M_G2C16H1_M": NaN, + "M_G2C16_M M_G2C16H2_M": NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.0311, + "M_G3C4_M M_G3C4H2_M": 0.028, + "M_G3C5_M M_G3C5H1_M": 0.9378, + "M_G3C5_M M_G3C5H2_M": 0.9612, + "M_G3N6C1_M M_G3N6C1H1_M": 0.9891, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9885, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9889, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9896, + "M_G3N6C2_M M_G3N6C2H2_M": 0.9888, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9882, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9888, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9875, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9891, + "M_G3_M M_G3H1_M": 0.0252, + "M_G3_M M_G3H2_M": 0.9707 + } +} \ No newline at end of file diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/FormFactorQuality.json b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/FormFactorQuality.json new file mode 100644 index 0000000000..2b998799cf --- /dev/null +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/FormFactorQuality.json @@ -0,0 +1 @@ +[0.4525, 92.7955] \ No newline at end of file diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/README.yaml b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/README.yaml index 1d80459c14..18ef33aad1 100644 --- a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/README.yaml +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/README.yaml @@ -143,3 +143,9 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-23' +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/SYSTEM_quality.json b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/SYSTEM_quality.json new file mode 100644 index 0000000000..b09389b199 --- /dev/null +++ b/Simulations/a95/28e/a9528e5501b2b41af2dd6f8540cb514a3eb186e0/5e86893c5c58e183eca1082084085205569a596b/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6585, "tails": 0.0, "total": 0.6585} \ No newline at end of file diff --git a/Simulations/afa/b24/afab24a3270f4289a86544d8f6e9b3bd72395d3e/5b4aadb79ec3804f4ca138b684e1cc23d7e3833b/README.yaml b/Simulations/afa/b24/afab24a3270f4289a86544d8f6e9b3bd72395d3e/5b4aadb79ec3804f4ca138b684e1cc23d7e3833b/README.yaml index 81d53f2ea4..b69ab5b221 100644 --- a/Simulations/afa/b24/afab24a3270f4289a86544d8f6e9b3bd72395d3e/5b4aadb79ec3804f4ca138b684e1cc23d7e3833b/README.yaml +++ b/Simulations/afa/b24/afab24a3270f4289a86544d8f6e9b3bd72395d3e/5b4aadb79ec3804f4ca138b684e1cc23d7e3833b/README.yaml @@ -28,8 +28,7 @@ AUTHORS_CONTACT: Thomas Piggot SYSTEM: 128DOPS_4480SOL_128SOD_303K_v1 SOFTWARE_VERSION: null FF: Berger -FF_SOURCE: starting structure from the CHARMM-GUI with the appropriate hydrogen atoms - removed +FF_SOURCE: starting structure from the CHARMM-GUI with the appropriate hydrogen atoms removed FF_DATE: null CPT: null LOG: null diff --git a/Simulations/b04/7ff/b047ffe7ca543800f5d13bc850bbb66924b7231b/76a77f734fea9fcca1189a8c5b4533a68d73ead5/README.yaml b/Simulations/b04/7ff/b047ffe7ca543800f5d13bc850bbb66924b7231b/76a77f734fea9fcca1189a8c5b4533a68d73ead5/README.yaml index ee7155b9e4..74929afffd 100644 --- a/Simulations/b04/7ff/b047ffe7ca543800f5d13bc850bbb66924b7231b/76a77f734fea9fcca1189a8c5b4533a68d73ead5/README.yaml +++ b/Simulations/b04/7ff/b047ffe7ca543800f5d13bc850bbb66924b7231b/76a77f734fea9fcca1189a8c5b4533a68d73ead5/README.yaml @@ -31,8 +31,9 @@ AUTHORS_CONTACT: Ollila O. H. Samuli; Ferreira Tiago; Topgaard Daniel SYSTEM: 44CHOL_84POPC_6794SOL_298K_Berger SOFTWARE_VERSION: 4.5 FF: Berger and Modified Höltje model for cholesterol -FF_SOURCE: http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X - for cholesterol +FF_SOURCE: >- + http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X for + cholesterol FF_DATE: null CPT: null LOG: null diff --git a/Simulations/b16/7e2/b167e26f39a390c69bc605c2217f732d854c6395/f5de1720a24e1896cf96afc94fc4ef028adc47d0/README.yaml b/Simulations/b16/7e2/b167e26f39a390c69bc605c2217f732d854c6395/f5de1720a24e1896cf96afc94fc4ef028adc47d0/README.yaml index 285baff153..52263666cd 100644 --- a/Simulations/b16/7e2/b167e26f39a390c69bc605c2217f732d854c6395/f5de1720a24e1896cf96afc94fc4ef028adc47d0/README.yaml +++ b/Simulations/b16/7e2/b167e26f39a390c69bc605c2217f732d854c6395/f5de1720a24e1896cf96afc94fc4ef028adc47d0/README.yaml @@ -31,8 +31,9 @@ AUTHORS_CONTACT: Ollila O. H. Samuli; Ferreira Tiago; Topgaard Daniel SYSTEM: 8CHOL_120POPC_7290SOL_298K_Berger SOFTWARE_VERSION: 4.5 FF: Berger and Modified Höltje model for cholesterol -FF_SOURCE: http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X - for cholesterol +FF_SOURCE: >- + http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X for + cholesterol FF_DATE: null CPT: null LOG: null diff --git a/Simulations/ba2/d98/ba2d9804e770c2c4d40c9f45981adbea446d17d5/ac4d43f168d107273573bbc106c35eb26b25a9c7/README.yaml b/Simulations/ba2/d98/ba2d9804e770c2c4d40c9f45981adbea446d17d5/ac4d43f168d107273573bbc106c35eb26b25a9c7/README.yaml index 3d3a324301..848a3610ae 100644 --- a/Simulations/ba2/d98/ba2d9804e770c2c4d40c9f45981adbea446d17d5/ac4d43f168d107273573bbc106c35eb26b25a9c7/README.yaml +++ b/Simulations/ba2/d98/ba2d9804e770c2c4d40c9f45981adbea446d17d5/ac4d43f168d107273573bbc106c35eb26b25a9c7/README.yaml @@ -11,8 +11,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_73CAL_146CLA_330K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/c51/b34/c51b34a37b0fc7a4b522441a10112b28411f80a4/38058dc73d22c28252a892fb9caced8f2220b4bf/README.yaml b/Simulations/c51/b34/c51b34a37b0fc7a4b522441a10112b28411f80a4/38058dc73d22c28252a892fb9caced8f2220b4bf/README.yaml index 11ec259ca3..ae45c8b8d0 100644 --- a/Simulations/c51/b34/c51b34a37b0fc7a4b522441a10112b28411f80a4/38058dc73d22c28252a892fb9caced8f2220b4bf/README.yaml +++ b/Simulations/c51/b34/c51b34a37b0fc7a4b522441a10112b28411f80a4/38058dc73d22c28252a892fb9caced8f2220b4bf/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 86CHOL_200POPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_FragmentQuality.json b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_FragmentQuality.json new file mode 100644 index 0000000000..863fc976c5 --- /dev/null +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_FragmentQuality.json @@ -0,0 +1 @@ +{"sn-1": NaN, "sn-2": NaN, "headgroup": 0.6337, "total": 0.6337} \ No newline at end of file diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_OrderParameters_quality.json b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_OrderParameters_quality.json new file mode 100644 index 0000000000..be1ccdee91 --- /dev/null +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/DPPC_OrderParameters_quality.json @@ -0,0 +1,84 @@ +{ + "10.1021/bi00687a021/1": { + "M_G1C10_M M_G1C10H1_M": NaN, + "M_G1C10_M M_G1C10H2_M": NaN, + "M_G1C11_M M_G1C11H1_M": NaN, + "M_G1C11_M M_G1C11H2_M": NaN, + "M_G1C12_M M_G1C12H1_M": NaN, + "M_G1C12_M M_G1C12H2_M": NaN, + "M_G1C13_M M_G1C13H1_M": NaN, + "M_G1C13_M M_G1C13H2_M": NaN, + "M_G1C14_M M_G1C14H1_M": NaN, + "M_G1C14_M M_G1C14H2_M": NaN, + "M_G1C15_M M_G1C15H1_M": NaN, + "M_G1C15_M M_G1C15H2_M": NaN, + "M_G1C16_M M_G1C16H1_M": NaN, + "M_G1C16_M M_G1C16H2_M": NaN, + "M_G1C17_M 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NaN, + "M_G2C17_M M_G2C17H1_M": NaN, + "M_G2C17_M M_G2C17H2_M": NaN, + "M_G2C17_M M_G2C17H3_M": NaN, + "M_G2C3_M M_G2C3H1_M": NaN, + "M_G2C3_M M_G2C3H2_M": NaN, + "M_G2C4_M M_G2C4H1_M": NaN, + "M_G2C4_M M_G2C4H2_M": NaN, + "M_G2C5_M M_G2C5H1_M": NaN, + "M_G2C5_M M_G2C5H2_M": NaN, + "M_G2C6_M M_G2C6H1_M": NaN, + "M_G2C6_M M_G2C6H2_M": NaN, + "M_G2C7_M M_G2C7H1_M": NaN, + "M_G2C7_M M_G2C7H2_M": NaN, + "M_G2C8_M M_G2C8H1_M": NaN, + "M_G2C8_M M_G2C8H2_M": NaN, + "M_G2C9_M M_G2C9H1_M": NaN, + "M_G2C9_M M_G2C9H2_M": NaN, + "M_G2_M M_G2H1_M": NaN, + "M_G3C4_M M_G3C4H1_M": 0.0474, + "M_G3C4_M M_G3C4H2_M": 0.0432, + "M_G3C5_M M_G3C5H1_M": 0.789, + "M_G3C5_M M_G3C5H2_M": 0.5155, + "M_G3N6C1_M M_G3N6C1H1_M": 0.986, + "M_G3N6C1_M M_G3N6C1H2_M": 0.9858, + "M_G3N6C1_M M_G3N6C1H3_M": 0.9846, + "M_G3N6C2_M M_G3N6C2H1_M": 0.9849, + "M_G3N6C2_M M_G3N6C2H2_M": 0.9861, + "M_G3N6C2_M M_G3N6C2H3_M": 0.9843, + "M_G3N6C3_M M_G3N6C3H1_M": 0.9853, + "M_G3N6C3_M M_G3N6C3H2_M": 0.9859, + "M_G3N6C3_M M_G3N6C3H3_M": 0.9868, + "M_G3_M M_G3H1_M": 0.3769, + "M_G3_M M_G3H2_M": 0.7643 + } +} \ No newline at end of file diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/FormFactorQuality.json b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/FormFactorQuality.json new file mode 100644 index 0000000000..5384d18279 --- /dev/null +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/FormFactorQuality.json @@ -0,0 +1 @@ +[0.0262, 77.1194] \ No newline at end of file diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/README.yaml b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/README.yaml index 525e964def..1af834306b 100644 --- a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/README.yaml +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/README.yaml @@ -143,3 +143,9 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-23' +EXPERIMENT: + ORDERPARAMETER: + DPPC: + - 10.1021/bi00687a021/1 + FORMFACTOR: + - 10.1016/j.bbamem.2011.07.022/4 diff --git a/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/SYSTEM_quality.json b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/SYSTEM_quality.json new file mode 100644 index 0000000000..77d2a59c82 --- /dev/null +++ b/Simulations/c54/a7f/c54a7fae3f5d01b83d2bdb3d42700185104e05eb/5a9808f2cedaec641ac9f872e539f852c81aa7fc/SYSTEM_quality.json @@ -0,0 +1 @@ +{"headgroup": 0.6337, "tails": 0.0, "total": 0.6337} \ No newline at end of file diff --git a/Simulations/c68/041/c680410d7e6010621242fd9ae5c9d1cd0e601997/641ca89d6f2450268ecb94cd0a688fb423bc6e9b/README.yaml b/Simulations/c68/041/c680410d7e6010621242fd9ae5c9d1cd0e601997/641ca89d6f2450268ecb94cd0a688fb423bc6e9b/README.yaml index 26e1235ee7..e4275696ff 100644 --- a/Simulations/c68/041/c680410d7e6010621242fd9ae5c9d1cd0e601997/641ca89d6f2450268ecb94cd0a688fb423bc6e9b/README.yaml +++ b/Simulations/c68/041/c680410d7e6010621242fd9ae5c9d1cd0e601997/641ca89d6f2450268ecb94cd0a688fb423bc6e9b/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_73CAL_146CLA_370K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/c8d/54f/c8d54fda73085e3f9685615b4cccc6a3dffc7442/62808d96749eaff3b5572316cb0fbaa4d0863267/README.yaml b/Simulations/c8d/54f/c8d54fda73085e3f9685615b4cccc6a3dffc7442/62808d96749eaff3b5572316cb0fbaa4d0863267/README.yaml index c88984bb4a..fce28c751d 100644 --- a/Simulations/c8d/54f/c8d54fda73085e3f9685615b4cccc6a3dffc7442/62808d96749eaff3b5572316cb0fbaa4d0863267/README.yaml +++ b/Simulations/c8d/54f/c8d54fda73085e3f9685615b4cccc6a3dffc7442/62808d96749eaff3b5572316cb0fbaa4d0863267/README.yaml @@ -32,8 +32,9 @@ AUTHORS_CONTACT: Ollila O. H. Samuli; Ferreira Tiago; Topgaard Daniel SYSTEM: 18CHOL_110POPC_8481SOL_298K_Berger SOFTWARE_VERSION: 4.5 FF: Berger and Modified Höltje model for cholesterol -FF_SOURCE: http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X - for cholesterol +FF_SOURCE: >- + http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X for + cholesterol FF_DATE: null CPT: null LOG: null diff --git a/Simulations/cda/5ce/cda5ce14c4374dd6a18f5f93ebcb02fb7893afdc/42632e1a93546847371b47eafbf6d0742a4aa445/README.yaml b/Simulations/cda/5ce/cda5ce14c4374dd6a18f5f93ebcb02fb7893afdc/42632e1a93546847371b47eafbf6d0742a4aa445/README.yaml index 067f62d203..6403ba4d11 100644 --- a/Simulations/cda/5ce/cda5ce14c4374dd6a18f5f93ebcb02fb7893afdc/42632e1a93546847371b47eafbf6d0742a4aa445/README.yaml +++ b/Simulations/cda/5ce/cda5ce14c4374dd6a18f5f93ebcb02fb7893afdc/42632e1a93546847371b47eafbf6d0742a4aa445/README.yaml @@ -12,8 +12,7 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 204DPPC_52CHOL_166DOPC_16880SOL_304SOD_304CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/ce7/224/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/README.yaml b/Simulations/ce7/224/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/README.yaml index c2fcd6bd67..a5367edfc0 100644 --- a/Simulations/ce7/224/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/README.yaml +++ b/Simulations/ce7/224/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/ce72249ff227687a3a83f82cde8c3aeaf0da0b9e/README.yaml @@ -24,8 +24,7 @@ AUTHORS_CONTACT: Kav, Batuhan SYSTEM: DOPC_nosalt_at_303K_with_AMOEBA SOFTWARE_VERSION: v7.5.1 FF: AMOEBA -FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in - publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 +FF_SOURCE: OpenMM version https://github.com/Inniag/openmm-scripts-amoeba used in publication https://doi.org/10.1021/jacs.0c02394, original parameters https://doi.org/10.1080/00268976.2018.1436201 FF_DATE: null TRAJECTORY_SIZE: 1373734948 TRJLENGTH: 201600.0 diff --git a/Simulations/ce8/76e/ce876e53c0e2f6f5fc73560b2bf1e8f43ea19817/cccb92e36638232a12c0d507f71f1ed737213a94/README.yaml b/Simulations/ce8/76e/ce876e53c0e2f6f5fc73560b2bf1e8f43ea19817/cccb92e36638232a12c0d507f71f1ed737213a94/README.yaml index a5be893299..945b37f7d4 100644 --- a/Simulations/ce8/76e/ce876e53c0e2f6f5fc73560b2bf1e8f43ea19817/cccb92e36638232a12c0d507f71f1ed737213a94/README.yaml +++ b/Simulations/ce8/76e/ce876e53c0e2f6f5fc73560b2bf1e8f43ea19817/cccb92e36638232a12c0d507f71f1ed737213a94/README.yaml @@ -6,8 +6,9 @@ PREEQTIME: 1.875 TIMELEFTOUT: 10 TEMPERATURE: 303.15 SYSTEM: DMPC -AUTHORS_CONTACT: Anna Kristine Sandtorv-Lerøen/anna.kristine.sandtorv.leroen@gmail.com - / Markus S. Miettinen/Markus.Miettinen@uib.no +AUTHORS_CONTACT: >- + Anna Kristine Sandtorv-Lerøen/anna.kristine.sandtorv.leroen@gmail.com / Markus S. + Miettinen/Markus.Miettinen@uib.no SOFTWARE_VERSION: '2026.1' FF: CHARMM36 FF_DATE: 14.04.2026 diff --git a/Simulations/d41/0a0/d410a0c257276ccda5fcc3b444ee87e7a41cc940/38ede40be484a826ca8af53369965277ebe29e43/README.yaml b/Simulations/d41/0a0/d410a0c257276ccda5fcc3b444ee87e7a41cc940/38ede40be484a826ca8af53369965277ebe29e43/README.yaml index 2e38e181dc..5f72f5f125 100644 --- a/Simulations/d41/0a0/d410a0c257276ccda5fcc3b444ee87e7a41cc940/38ede40be484a826ca8af53369965277ebe29e43/README.yaml +++ b/Simulations/d41/0a0/d410a0c257276ccda5fcc3b444ee87e7a41cc940/38ede40be484a826ca8af53369965277ebe29e43/README.yaml @@ -143,3 +143,7 @@ bioschema_properties: doi: 10.5281/zenodo.10635500 spdxLicenseList: 3.29.0 retrieved: '2026-09-23' +EXPERIMENT: + ORDERPARAMETER: + DPPC: [] + FORMFACTOR: [] diff --git a/Simulations/d44/b08/d44b08236b42139f46a3fbbbd840e239070fb0b8/60bc71c1212d826e4842a448c90cbd8506142e69/README.yaml b/Simulations/d44/b08/d44b08236b42139f46a3fbbbd840e239070fb0b8/60bc71c1212d826e4842a448c90cbd8506142e69/README.yaml index 064dee08ee..b22410d019 100644 --- a/Simulations/d44/b08/d44b08236b42139f46a3fbbbd840e239070fb0b8/60bc71c1212d826e4842a448c90cbd8506142e69/README.yaml +++ b/Simulations/d44/b08/d44b08236b42139f46a3fbbbd840e239070fb0b8/60bc71c1212d826e4842a448c90cbd8506142e69/README.yaml @@ -19,8 +19,9 @@ COMPOSITION: COUNT: 10623 MAPPING: mappingTIP3Pwater.yaml DIR_WRK: /usr/home/bort/Databank -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Gola, Adrien; Marques, Carlos; Benzerara, - Olivier; Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Gola, Adrien; Marques, Carlos; Benzerara, Olivier; Thalmann, + Fabrice SYSTEM: 64DPPC_10623SOL_288K SOFTWARE_VERSION: 2016.4 FF: CHARMM36 diff --git a/Simulations/d7d/10b/d7d10b044a4dca1837d9aed145f288a1549073f7/235d29651e1726b997a486036fecc6dec41f60e3/README.yaml b/Simulations/d7d/10b/d7d10b044a4dca1837d9aed145f288a1549073f7/235d29651e1726b997a486036fecc6dec41f60e3/README.yaml index e4628f344c..d251a7dc19 100644 --- a/Simulations/d7d/10b/d7d10b044a4dca1837d9aed145f288a1549073f7/235d29651e1726b997a486036fecc6dec41f60e3/README.yaml +++ b/Simulations/d7d/10b/d7d10b044a4dca1837d9aed145f288a1549073f7/235d29651e1726b997a486036fecc6dec41f60e3/README.yaml @@ -12,8 +12,7 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200DOPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/d8d/348/d8d348469625cce7a89646ba7160b7a89655bca9/9ef0a1a56cee2c014dea0be3ed2312ea264ca1e7/README.yaml b/Simulations/d8d/348/d8d348469625cce7a89646ba7160b7a89655bca9/9ef0a1a56cee2c014dea0be3ed2312ea264ca1e7/README.yaml index 8d5837c5e8..5ebb9bfdfb 100644 --- a/Simulations/d8d/348/d8d348469625cce7a89646ba7160b7a89655bca9/9ef0a1a56cee2c014dea0be3ed2312ea264ca1e7/README.yaml +++ b/Simulations/d8d/348/d8d348469625cce7a89646ba7160b7a89655bca9/9ef0a1a56cee2c014dea0be3ed2312ea264ca1e7/README.yaml @@ -1,5 +1,5 @@ -AUTHORS_CONTACT: Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; - Thalmann, Fabrice +AUTHORS_CONTACT: >- + Walter, Vivien; Ruscher, Celine; Benzerara, Olivier; Marques, Carlos; Thalmann, Fabrice FF_DATE: June 2015 SYSTEM: 212DPPC_29826SOL_318K TYPEOFSYSTEM: lipid bilayer diff --git a/Simulations/d93/702/d9370247c9468b63f2c1d64c795b08051f775195/8f80b92eb5371214ccb487d53ce1fb313800076c/README.yaml b/Simulations/d93/702/d9370247c9468b63f2c1d64c795b08051f775195/8f80b92eb5371214ccb487d53ce1fb313800076c/README.yaml index 2ac831a4cd..6032f3820a 100644 --- a/Simulations/d93/702/d9370247c9468b63f2c1d64c795b08051f775195/8f80b92eb5371214ccb487d53ce1fb313800076c/README.yaml +++ b/Simulations/d93/702/d9370247c9468b63f2c1d64c795b08051f775195/8f80b92eb5371214ccb487d53ce1fb313800076c/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 50CHOL_200POPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/da3/d85/da3d859f724f78b3b654d485024e5f3cb803dbb6/f99aed4d2d27d16c580928f1e438e7974bade4e6/README.yaml b/Simulations/da3/d85/da3d859f724f78b3b654d485024e5f3cb803dbb6/f99aed4d2d27d16c580928f1e438e7974bade4e6/README.yaml index 1ea0c01a5a..84e5a6f96e 100644 --- a/Simulations/da3/d85/da3d859f724f78b3b654d485024e5f3cb803dbb6/f99aed4d2d27d16c580928f1e438e7974bade4e6/README.yaml +++ b/Simulations/da3/d85/da3d859f724f78b3b654d485024e5f3cb803dbb6/f99aed4d2d27d16c580928f1e438e7974bade4e6/README.yaml @@ -12,8 +12,7 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 204DPPC_52CHOL_166DOPC_16880SOL_46SOD_46CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/dd9/c59/dd9c5964efd8e2840736332b5a938932f12beebc/ed59622747ff6ef7329188dd62173852cdab20fd/README.yaml b/Simulations/dd9/c59/dd9c5964efd8e2840736332b5a938932f12beebc/ed59622747ff6ef7329188dd62173852cdab20fd/README.yaml index e2fad1913e..607eb9f807 100644 --- a/Simulations/dd9/c59/dd9c5964efd8e2840736332b5a938932f12beebc/ed59622747ff6ef7329188dd62173852cdab20fd/README.yaml +++ b/Simulations/dd9/c59/dd9c5964efd8e2840736332b5a938932f12beebc/ed59622747ff6ef7329188dd62173852cdab20fd/README.yaml @@ -12,8 +12,7 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200DOPC_9000SOL_73CAL_146CLA_293K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Kohagen for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/dfb/5bf/dfb5bf1081781764f77b579e48058942806902e2/3cd2151fd09332fdd650b78a0bc3950479464b08/README.yaml b/Simulations/dfb/5bf/dfb5bf1081781764f77b579e48058942806902e2/3cd2151fd09332fdd650b78a0bc3950479464b08/README.yaml index b060473f34..e52911205f 100644 --- a/Simulations/dfb/5bf/dfb5bf1081781764f77b579e48058942806902e2/3cd2151fd09332fdd650b78a0bc3950479464b08/README.yaml +++ b/Simulations/dfb/5bf/dfb5bf1081781764f77b579e48058942806902e2/3cd2151fd09332fdd650b78a0bc3950479464b08/README.yaml @@ -32,8 +32,9 @@ AUTHORS_CONTACT: Ollila, Samuli SYSTEM: 90POPC_38PAzePCprot_7632SOL_298K SOFTWARE_VERSION: 4.5 FF: Berger -FF_SOURCE: H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 - – 2743, http://dx.doi.org/10.1016/j.bpj.2009.01.007 for PAzePCprot +FF_SOURCE: >- + H. Khandelia and O. G. Mouritsen, Biophysical Journal, 2009, 96(7), 2734 – 2743, + http://dx.doi.org/10.1016/j.bpj.2009.01.007 for PAzePCprot FF_DATE: null CPT: null LOG: null diff --git a/Simulations/ebb/ca8/ebbca82ace6baca0eba4d8e154196c49dddef206/bd232347e593006376a2344ec2e97ffa5655f20c/README.yaml b/Simulations/ebb/ca8/ebbca82ace6baca0eba4d8e154196c49dddef206/bd232347e593006376a2344ec2e97ffa5655f20c/README.yaml index 48eb5fd096..88e180214a 100644 --- a/Simulations/ebb/ca8/ebbca82ace6baca0eba4d8e154196c49dddef206/bd232347e593006376a2344ec2e97ffa5655f20c/README.yaml +++ b/Simulations/ebb/ca8/ebbca82ace6baca0eba4d8e154196c49dddef206/bd232347e593006376a2344ec2e97ffa5655f20c/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 22CHOL_200POPC_9000SOL_21SOD_21CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/f07/1aa/f071aa10d13d9eca665430308082317769f4172e/22e6c3544690d4405b6933bf77972a73009ae9ac/README.yaml b/Simulations/f07/1aa/f071aa10d13d9eca665430308082317769f4172e/22e6c3544690d4405b6933bf77972a73009ae9ac/README.yaml index 6a5d01afa2..e144d77b08 100644 --- a/Simulations/f07/1aa/f071aa10d13d9eca665430308082317769f4172e/22e6c3544690d4405b6933bf77972a73009ae9ac/README.yaml +++ b/Simulations/f07/1aa/f071aa10d13d9eca665430308082317769f4172e/22e6c3544690d4405b6933bf77972a73009ae9ac/README.yaml @@ -6,8 +6,9 @@ PREEQTIME: 1.875 TIMELEFTOUT: 7 TEMPERATURE: 303.15 SYSTEM: DMPC -AUTHORS_CONTACT: Anna Kristine Sandtorv-Leroen/anna.kristine.sandtorv.leroen@gmail.com - / Markus S. Miettinen/Markus.Miettinen@uib.no +AUTHORS_CONTACT: >- + Anna Kristine Sandtorv-Leroen/anna.kristine.sandtorv.leroen@gmail.com / Markus S. + Miettinen/Markus.Miettinen@uib.no SOFTWARE_VERSION: '2026.1' FF: Lipid21(AMBER) FF_SOURCE: CHARMM-GUI diff --git a/Simulations/f5d/6d3/f5d6d3f7e54bde318254a0476d92b40cf73b92a2/5c2318b611ae263ecdd773eb635f193b38737105/README.yaml b/Simulations/f5d/6d3/f5d6d3f7e54bde318254a0476d92b40cf73b92a2/5c2318b611ae263ecdd773eb635f193b38737105/README.yaml index 930f2ab525..2f57a3c297 100644 --- a/Simulations/f5d/6d3/f5d6d3f7e54bde318254a0476d92b40cf73b92a2/5c2318b611ae263ecdd773eb635f193b38737105/README.yaml +++ b/Simulations/f5d/6d3/f5d6d3f7e54bde318254a0476d92b40cf73b92a2/5c2318b611ae263ecdd773eb635f193b38737105/README.yaml @@ -12,8 +12,7 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200DOPC_9000SOL_21SOD_21CLA_293K SOFTWARE_VERSION: 4.6 FF: Slipids for lipids and Smith & Dang for ions -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null diff --git a/Simulations/f62/739/f627391cd6cddf82078a7a12c4cd22767535b6fe/d9c93bb0ae93ede37c230593a348691012519efc/README.yaml b/Simulations/f62/739/f627391cd6cddf82078a7a12c4cd22767535b6fe/d9c93bb0ae93ede37c230593a348691012519efc/README.yaml index 5ac8e0ef98..49d13767ec 100644 --- a/Simulations/f62/739/f627391cd6cddf82078a7a12c4cd22767535b6fe/d9c93bb0ae93ede37c230593a348691012519efc/README.yaml +++ b/Simulations/f62/739/f627391cd6cddf82078a7a12c4cd22767535b6fe/d9c93bb0ae93ede37c230593a348691012519efc/README.yaml @@ -32,8 +32,9 @@ AUTHORS_CONTACT: Ollila O. H. Samuli; Ferreira Tiago; Topgaard Daniel SYSTEM: 64CHOL_64POPC_10314SOL_298K_Berger SOFTWARE_VERSION: 4.5 FF: Berger and Modified Höltje model for cholesterol -FF_SOURCE: http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X - for cholesterol +FF_SOURCE: >- + http://wcm.ucalgary.ca/tieleman/downloads; http://dx.doi.org/10.1016/S0005-2736(01)00270-X for + cholesterol FF_DATE: null CPT: null LOG: null diff --git a/Simulations/f77/7b3/f777b331c6644fa590a844c27121e5faca644413/97b177a99817aaa63cad63d3f51a70722a3f74d6/README.yaml b/Simulations/f77/7b3/f777b331c6644fa590a844c27121e5faca644413/97b177a99817aaa63cad63d3f51a70722a3f74d6/README.yaml index 8be9c4cd51..edcf640a2b 100644 --- a/Simulations/f77/7b3/f777b331c6644fa590a844c27121e5faca644413/97b177a99817aaa63cad63d3f51a70722a3f74d6/README.yaml +++ b/Simulations/f77/7b3/f777b331c6644fa590a844c27121e5faca644413/97b177a99817aaa63cad63d3f51a70722a3f74d6/README.yaml @@ -12,8 +12,8 @@ AUTHORS_CONTACT: Javanainen, Matti SYSTEM: 200POPC_9000SOL_73CAL_146CLA_310K SOFTWARE_VERSION: 4.6 FF: Slipids with ECC-scaled ions (Kohagen) -FF_SOURCE: http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ - for ions +FF_SOURCE: >- + http://www.fos.su.se/~sasha/SLipids/ for lipids and https://bitbucket.org/hseara/ions/ for ions FF_DATE: pre-2020 CPT: null LOG: null